From c2f20e4bdab7f596485ca225de517dc096067dc8 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Fri, 23 Aug 2024 11:15:13 -0500 Subject: [PATCH 01/30] ci: Attempt to split everything out Don't hate me Adam --- .github/workflows/lint.yml | 157 ++++++ .github/workflows/nf-test.yml | 270 +++++++++ .github/workflows/pytest-workflow.yml | 343 ++++++++++++ .github/workflows/test.yml | 778 -------------------------- 4 files changed, 770 insertions(+), 778 deletions(-) create mode 100644 .github/workflows/lint.yml create mode 100644 .github/workflows/nf-test.yml create mode 100644 .github/workflows/pytest-workflow.yml delete mode 100644 .github/workflows/test.yml diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml new file mode 100644 index 00000000000..185916f517d --- /dev/null +++ b/.github/workflows/lint.yml @@ -0,0 +1,157 @@ +name: Run Linting +on: + pull_request: + branches: [master] + merge_group: + types: [checks_requested] + branches: [master] + workflow_dispatch: + inputs: + runners: + description: "Runners to test on" + type: choice + options: + - "ubuntu-latest" + - "self-hosted" + default: "self-hosted" + +# Cancel if a newer run is started +concurrency: + group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} + cancel-in-progress: true + +env: + NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity + NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + +jobs: + pre-commit: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4 + - uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f # v5 + - uses: pre-commit/action@2c7b3805fd2a0fd8c1884dcaebf91fc102a13ecd # v3.0.1 + # FIXME Flip this off once we get to less than a couple hundred. Adding + # this so it will only run against changed files. It'll make it much + # easier to fix these as they come up rather than everything at once. + with: + extra_args: "" + + prettier: + runs-on: ubuntu-latest + steps: + - name: Check out repository + uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4 + + - name: Install NodeJS + uses: actions/setup-node@1e60f620b9541d16bece96c5465dc8ee9832be0b # v4 + with: + node-version: "20" + + - name: Install Prettier + run: npm install -g prettier@3.1.0 + + - name: Run Prettier --check + run: prettier --check . + + editorconfig: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4 + + - uses: actions/setup-node@1e60f620b9541d16bece96c5465dc8ee9832be0b # v4 + with: + node-version: "20" + + - name: Install editorconfig-checker + run: npm install -g editorconfig-checker + + - name: Run ECLint check + run: editorconfig-checker -exclude README.md $(git ls-files | grep -v test) + + # FIXME Lint everything? + nf-core-lint-modules: + runs-on: ${{ github.event.inputs.runners || 'self-hosted' }} + name: nf-core-lint-modules + needs: [pytest-changes, nf-test-changes] + if: ${{ (needs.pytest-changes.outputs.modules != '[]') || ( needs.nf-test-changes.outputs.modules != '[]') }} + strategy: + fail-fast: false + matrix: + tags: + [ + "${{ fromJson(needs.pytest-changes.outputs.modules) }}", + "${{ fromJson(needs.nf-test-changes.outputs.modules) }}", + ] + steps: + - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4 + + - name: Set up Python + uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f # v5 + with: + python-version: "3.11" + + - uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4 + id: cache-pip + with: + path: ~/.cache/pip + key: ${{ runner.os }}-pip + restore-keys: | + ${{ runner.os }}-pip + + - name: Install pip + run: python -m pip install --upgrade pip + + - uses: actions/setup-java@b36c23c0d998641eff861008f374ee103c25ac73 # v4 + with: + distribution: "temurin" + java-version: "17" + + - name: Setup Nextflow + uses: nf-core/setup-nextflow@v2 + + - name: Install nf-core tools development version + run: python -m pip install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git@dev + + - name: Lint module ${{ matrix.tags }} + run: nf-core modules lint ${{ matrix.tags }} + + # FIXME Lint everything? + nf-core-lint-subworkflows: + runs-on: ubuntu-latest + name: nf-core-lint-modules + needs: [pytest-changes, nf-test-changes] + if: ${{ (needs.pytest-changes.outputs.subworkflows != '[]') || ( needs.nf-test-changes.outputs.subworkflows != '[]') }} + strategy: + fail-fast: false + matrix: + tags: + [ + "${{ fromJson(needs.pytest-changes.outputs.subworkflows) }}", + "${{ fromJson(needs.nf-test-changes.outputs.subworkflows) }}", + ] + steps: + - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4 + + - name: Set up Python + uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f # v5 + with: + python-version: "3.11" + + - name: Install pip + run: python -m pip install --upgrade pip + + - uses: actions/setup-java@b36c23c0d998641eff861008f374ee103c25ac73 # v4 + with: + distribution: "temurin" + java-version: "17" + + - name: Setup Nextflow + uses: nf-core/setup-nextflow@561fcfc7146dcb12e3871909b635ab092a781f34 # v2 + + - name: Install nf-core tools development version + run: python -m pip install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git@dev + + - name: Lint module ${{ matrix.tags }} + run: nf-core subworkflows lint ${{ matrix.tags }} diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml new file mode 100644 index 00000000000..764c2295b66 --- /dev/null +++ b/.github/workflows/nf-test.yml @@ -0,0 +1,270 @@ +name: Run tests +on: + pull_request: + branches: [master] + merge_group: + types: [checks_requested] + branches: [master] + workflow_dispatch: + inputs: + runners: + description: "Runners to test on" + type: choice + options: + - "ubuntu-latest" + - "self-hosted" + default: "self-hosted" + +# Cancel if a newer run is started +concurrency: + group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} + cancel-in-progress: true + +env: + NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity + NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + +jobs: + nf-test: + runs-on: ${{ github.event.inputs.runners || 'self-hosted' }} + name: nf-test + needs: [nf-test-changes] + if: ( needs.nf-test-changes.outputs.paths != '[]' ) + strategy: + fail-fast: false + matrix: + path: ["${{ fromJson(needs.nf-test-changes.outputs.paths) }}"] + profile: [conda, docker_self_hosted, singularity] + exclude: + - path: modules/nf-core/nf-test + - profile: conda + path: modules/nf-core/angsd/gl + - profile: conda + path: modules/nf-core/annotsv/installannotations + - profile: conda + path: modules/nf-core/happy/sompy + - profile: conda + path: modules/nf-core/backsub + - profile: conda + path: modules/nf-core/bakta/bakta + - profile: conda + path: modules/nf-core/bakta/baktadbdownload + - profile: conda + path: modules/nf-core/bases2fastq + - profile: conda + path: modules/nf-core/bcl2fastq + - profile: conda + path: modules/nf-core/bclconvert + - profile: conda + path: modules/nf-core/celesta + - profile: conda + path: modules/nf-core/cellpose + - profile: conda + path: modules/nf-core/cellranger/count + - profile: conda + path: modules/nf-core/cellranger/mkfastq + - profile: conda + path: modules/nf-core/cellranger/mkgtf + - profile: conda + path: modules/nf-core/cellranger/mkref + - profile: conda + path: modules/nf-core/cellranger/mkvdjref + - profile: conda + path: modules/nf-core/cellranger/multi + - profile: conda + path: modules/nf-core/cellranger/vdj + - profile: conda + path: modules/nf-core/checkqc + - profile: conda + path: modules/nf-core/custom/dumpsoftwareversions + - profile: conda + path: modules/nf-core/deepcell/mesmer + - profile: conda + path: modules/nf-core/deepvariant + - profile: conda + path: modules/nf-core/ensemblvep/vep + - profile: conda + path: modules/nf-core/fastk/fastk + - profile: conda + path: modules/nf-core/fastk/histex + - profile: conda + path: modules/nf-core/fastk/merge + - profile: conda + path: modules/nf-core/fcs/fcsadaptor + - profile: conda + path: modules/nf-core/fcs/fcsgx + - profile: conda + path: modules/nf-core/ganon/buildcustom + - profile: conda + path: modules/nf-core/ganon/classify + - profile: conda + path: modules/nf-core/ganon/report + - profile: conda + path: modules/nf-core/ganon/table + - profile: conda + path: modules/nf-core/gatk4/cnnscorevariants + - profile: conda + path: modules/nf-core/gatk4/determinegermlinecontigploidy + - profile: conda + path: modules/nf-core/genescopefk + - profile: conda + path: modules/nf-core/ilastik/multicut + - profile: conda + path: modules/nf-core/ilastik/pixelclassification + - profile: conda + path: modules/nf-core/imputeme/vcftoprs + - profile: conda + path: modules/nf-core/mcquant + - profile: conda + path: modules/nf-core/merquryfk/katcomp + - profile: conda + path: modules/nf-core/merquryfk/katgc + - profile: conda + path: modules/nf-core/merquryfk/merquryfk + - profile: conda + path: modules/nf-core/merquryfk/ploidyplot + - profile: conda + path: modules/nf-core/molkartgarage/clahe + - profile: conda + path: modules/nf-core/quartonotebook + - profile: conda + path: modules/nf-core/scimap/spatiallda + - profile: conda + path: modules/nf-core/sentieon/bwaindex + - profile: conda + path: modules/nf-core/sentieon/bwamem + - profile: conda + path: modules/nf-core/sentieon/dedup + - profile: conda + path: modules/nf-core/sentieon/qualcal + - profile: conda + path: modules/nf-core/spaceranger/mkgtf + - profile: conda + path: modules/nf-core/spaceranger/mkref + - profile: conda + path: modules/nf-core/spaceranger/count + - profile: conda + path: modules/nf-core/spotiflow + - profile: conda + path: modules/nf-core/svanalyzer/svbenchmark + - profile: conda + path: modules/nf-core/universc + - profile: singularity + path: modules/nf-core/universc + - profile: conda + path: modules/nf-core/vt/decompose + - profile: singularity + path: modules/nf-core/bases2fastq + - profile: conda + path: modules/nf-core/wittyer + - profile: conda + path: modules/nf-core/islandpath + - profile: conda + path: subworkflows/nf-core/vcf_annotate_ensemblvep + - profile: conda + path: subworkflows/nf-core/bcl_demultiplex + - profile: conda + path: subworkflows/nf-core/fastq_align_bamcmp_bwa + - profile: conda + path: subworkflows/nf-core/fastq_align_bwa + env: + NXF_ANSI_LOG: false + NFTEST_VER: "0.9.0" + SENTIEON_LICENSE_MESSAGE: ${{ secrets.SENTIEON_LICENSE_MESSAGE }} + SENTIEON_ENCRYPTION_KEY: ${{ secrets.SENTIEON_ENCRYPTION_KEY }} + + steps: + - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4 + + - uses: actions/setup-java@b36c23c0d998641eff861008f374ee103c25ac73 # v4 + with: + distribution: "temurin" + java-version: "17" + - name: Setup Nextflow + uses: nf-core/setup-nextflow@v2 + + - name: Install nf-test + uses: nf-core/setup-nf-test@v1 + + - name: Setup apptainer + if: matrix.profile == 'singularity' + uses: eWaterCycle/setup-apptainer@main + + - name: Set up Singularity + if: matrix.profile == 'singularity' + run: | + mkdir -p $NXF_SINGULARITY_CACHEDIR + mkdir -p $NXF_SINGULARITY_LIBRARYDIR + + - name: Set up Python + uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f # v5 + with: + python-version: "3.11" + + - uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4 + id: cache-pip-pdiff + with: + path: ~/.cache/pip + key: ${{ runner.os }}-pip-pdiff + restore-keys: | + ${{ runner.os }}-pip-pdiff + + - name: Install Python dependencies + run: python -m pip install --upgrade pip pdiff cryptography + + - name: Set up miniconda + if: matrix.profile == 'conda' + uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3 + with: + miniconda-version: "latest" + auto-update-conda: true + channels: conda-forge,bioconda,defaults + + - name: Conda setup + if: matrix.profile == 'conda' + run: | + conda clean -a + conda install -n base conda-libmamba-solver + conda config --set solver libmamba + echo $(realpath $CONDA)/condabin >> $GITHUB_PATH + echo $(realpath python) >> $GITHUB_PATH + + # Set up secrets + - name: Set up nextflow secrets + # TODO Only run if the tag includes `sentieon` + if: env.SENTIEON_ENCRYPTION_KEY != null && env.SENTIEON_LICENSE_MESSAGE != null + run: | + nextflow secrets set SENTIEON_AUTH_DATA $(python3 tests/modules/nf-core/sentieon/license_message.py encrypt --key "${{ secrets.SENTIEON_ENCRYPTION_KEY }}" --message "${{ secrets.SENTIEON_LICENSE_MESSAGE }}") + + # Test the module + - name: Run nf-test + env: + NFT_DIFF: "pdiff" + NFT_DIFF_ARGS: "--line-numbers --width 120 --expand-tabs=2" + SENTIEON_LICSRVR_IP: ${{ secrets.SENTIEON_LICSRVR_IP }} + SENTIEON_AUTH_MECH: "GitHub Actions - token" + run: | + # use "docker_self_hosted" if it runs on self-hosted runner and matrix.profile=docker + if [ "${{ matrix.profile }}" == "docker" ]; then + PROFILE="docker_self_hosted" + else + PROFILE=${{ matrix.profile }} + fi + + NFT_WORKDIR=~ \ + nf-test test \ + --profile=${{ matrix.profile }} \ + --tap=test.tap \ + --verbose \ + ${{ matrix.path }} + + - uses: pcolby/tap-summary@0959cbe1d4422e62afc65778cdaea6716c41d936 # v1 + with: + path: >- + test.tap + + - name: Clean up + if: always() + run: | + sudo rm -rf /home/ubuntu/tests/ diff --git a/.github/workflows/pytest-workflow.yml b/.github/workflows/pytest-workflow.yml new file mode 100644 index 00000000000..23522d5529b --- /dev/null +++ b/.github/workflows/pytest-workflow.yml @@ -0,0 +1,343 @@ +name: Run tests +on: + pull_request: + branches: [master] + merge_group: + types: [checks_requested] + branches: [master] + workflow_dispatch: + inputs: + runners: + description: "Runners to test on" + type: choice + options: + - "ubuntu-latest" + - "self-hosted" + default: "self-hosted" + +# Cancel if a newer run is started +concurrency: + group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} + cancel-in-progress: true + +env: + NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity + NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + +jobs: + pytest-changes: + name: pytest-changes + runs-on: ubuntu-latest + outputs: + tags: ${{ steps.filter.outputs.changes }} + modules: ${{ steps.tags.outputs.modules }} + subworkflows: ${{ steps.tags.outputs.subworkflows }} + steps: + - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4 + with: + fetch-depth: 2 # To retrieve the preceding commit. + + # TODO: change back to using dorny/paths-filter when https://github.com/dorny/paths-filter/pull/133 is implemented + - uses: mirpedrol/paths-filter@main + id: filter + with: + filters: "tests/config/pytest_modules.yml" + token: "" + + - name: Fetch module tags + id: tags + run: | + echo modules=$(echo '${{ steps.filter.outputs.changes }}' | jq -c '. | map(select(contains("modules"))) | map(gsub("modules/"; ""))') >> $GITHUB_OUTPUT + echo subworkflows=$(echo '${{ steps.filter.outputs.changes }}' | jq '. | map(select(contains("subworkflow"))) | map(gsub("subworkflows/"; ""))') >> $GITHUB_OUTPUT + + - name: debug + run: | + echo ${{ steps.tags.outputs.modules }} + echo ${{ steps.tags.outputs.subworkflows }} + + pytest: + runs-on: ${{ github.event.inputs.runners || 'self-hosted' }} + name: pytest + needs: [pytest-changes] + if: needs.pytest-changes.outputs.tags != '[]' + strategy: + fail-fast: false + matrix: + tags: ["${{ fromJson(needs.pytest-changes.outputs.tags) }}"] + profile: [conda, docker, singularity] + exclude: + - tags: nf-test + - profile: conda + tags: backsub + - profile: conda + tags: bases2fastq + - profile: singularity + tags: bases2fastq + - profile: conda + tags: basicpy + - profile: conda + tags: bcl2fastq + - profile: conda + tags: bclconvert + - profile: conda + tags: bwa/aln + - profile: conda + tags: bwa/index + - profile: conda + tags: bwa/mem + - profile: conda + tags: bwa/sampe + - profile: conda + tags: bwa/samse + - profile: conda + tags: cellpose + - profile: conda + tags: cellrangerarc/count + - profile: conda + tags: cellrangerarc/mkfastq + - profile: conda + tags: cellrangerarc/mkgtf + - profile: conda + tags: cellrangerarc/mkref + - profile: conda + tags: cellrangeratac/count + - profile: conda + tags: cellrangeratac/mkfastq + - profile: conda + tags: cellrangeratac/mkref + - profile: conda + tags: checkm2/databasedownload + - profile: conda + tags: checkm2/predict + - profile: conda + tags: controlfreec/makegraph2 + - profile: conda + tags: coreograph + - profile: conda + tags: deepcell/mesmer + - profile: conda + tags: deepvariant + - profile: conda + tags: fastani + - profile: conda + tags: fastk/fastk + - profile: conda + tags: fastk/histex + - profile: conda + tags: fastk/merge + - profile: conda + tags: fcs/fcsadaptor + - profile: conda + tags: fcs/fcsgx + - profile: conda + tags: gatk4/cnnscorevariants + - profile: conda + tags: gatk4/determinegermlinecontigploidy + - profile: singularity + tags: gatk4/determinegermlinecontigploidy + - profile: conda + tags: gatk4/germlinecnvcaller + - profile: conda + tags: gatk4/postprocessgermlinecnvcalls + - profile: conda + tags: genescopefk + - profile: conda + tags: happy/sompy + - profile: conda + tags: hlala/preparegraph + - profile: conda + tags: ilastik/multicut + - profile: conda + tags: ilastik/pixelclassification + - profile: conda + tags: imputeme/vcftoprs + - profile: conda + tags: islandpath + - profile: conda + tags: manta/convertinversion + - profile: conda + tags: mcquant + - profile: conda + tags: medaka + - profile: conda + tags: merquryfk/katcomp + - profile: conda + tags: merquryfk/katgc + - profile: conda + tags: merquryfk/merquryfk + - profile: conda + tags: merquryfk/ploidyplot + - profile: conda + tags: minimap2/align + - profile: conda + tags: mitohifi/findmitoreference + - profile: conda + tags: mitohifi/mitohifi + - profile: conda + tags: nanoplot + - profile: conda + tags: ncbitools/vecscreen + - profile: conda + tags: parabricks/applybqsr + - profile: conda + tags: parabricks/dbsnp + - profile: conda + tags: parabricks/deepvariant + - profile: conda + tags: parabricks/fq2bam + - profile: conda + tags: parabricks/genotypegvcf + - profile: conda + tags: parabricks/haplotypecaller + - profile: conda + tags: parabricks/indexgvcf + - profile: conda + tags: parabricks/mutectcaller + - profile: conda + tags: picard/collecthsmetrics + - profile: conda + tags: picard/collectwgsmetrics + - profile: conda + tags: scimap/mcmicro + - profile: conda + tags: sentieon/applyvarcal + - profile: conda + tags: sentieon/datametrics + - profile: conda + tags: sentieon/dnamodelapply + - profile: conda + tags: sentieon/dnascope + - profile: conda + tags: sentieon/readwriter + - profile: conda + tags: sentieon/tnfilter + - profile: conda + tags: sentieon/tnhaplotyper2 + - profile: conda + tags: sentieon/tnscope + - profile: conda + tags: sentieon/varcal + - profile: conda + tags: sentieon/wgsmetrics + - profile: conda + tags: subworkflows/bam_qc_picard + - profile: conda + tags: subworkflows/bcl_demultiplex + - profile: conda + tags: subworkflows/fasta_clean_fcs + - profile: conda + tags: svanalyzer/svbenchmark + - profile: conda + tags: universc + - profile: singularity + tags: universc + - profile: conda + tags: vt/decompose + env: + NXF_ANSI_LOG: false + + steps: + - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4 + + - name: Set up Python + uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f # v5 + with: + python-version: "3.11" + + - uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4 + id: cache-pip-pytest + with: + path: ~/.cache/pip + key: ${{ runner.os }}-pip-pytest + restore-keys: | + ${{ runner.os }}-pip-pytest + + - name: Install Python dependencies + run: python -m pip install --upgrade pip pytest-workflow cryptography + + - uses: actions/setup-java@b36c23c0d998641eff861008f374ee103c25ac73 # v4 + with: + distribution: "temurin" + java-version: "17" + - name: Setup Nextflow ${{ matrix.NXF_VER }} + uses: nf-core/setup-nextflow@v2 + with: + version: "${{ matrix.NXF_VER }}" + + - name: Setup apptainer + if: matrix.profile == 'singularity' + uses: eWaterCycle/setup-apptainer@main + + - name: Set up Singularity + if: matrix.profile == 'singularity' + run: | + mkdir -p $NXF_SINGULARITY_CACHEDIR + mkdir -p $NXF_SINGULARITY_LIBRARYDIR + + - name: Set up miniconda + uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3 + with: + miniconda-version: "latest" + channels: conda-forge,bioconda,defaults + python-version: ${{ matrix.python-version }} + + - name: Conda setup + run: | + conda clean -a + conda install -n base conda-libmamba-solver + conda config --set solver libmamba + echo $(realpath $CONDA)/condabin >> $GITHUB_PATH + echo $(realpath python) >> $GITHUB_PATH + + # Test the module + - name: Run pytest-workflow + # only use one thread for pytest-workflow to avoid race condition on conda cache. + run: TMPDIR=~ PROFILE=${{ matrix.profile }} pytest --tag ${{ matrix.tags }} --symlink --kwdof --git-aware --color=yes + + - name: Output log on failure + if: failure() + run: | + sudo apt-get update > /dev/null + sudo apt-get install bat > /dev/null + batcat --decorations=always --color=always /home/ubuntu/pytest_workflow_*/*/log.{out,err} + + - name: Setting global variables + uses: actions/github-script@60a0d83039c74a4aee543508d2ffcb1c3799cdea # v7 + id: parsed + with: + script: | + return '${{ matrix.tags }}'.toLowerCase().replaceAll(/\//g, '-').trim('-').trim('"') + result-encoding: string + + - name: Upload logs on failure + if: failure() + uses: actions/upload-artifact@834a144ee995460fba8ed112a2fc961b36a5ec5a # v4 + with: + name: logs-${{ matrix.profile }}-${{ steps.parsed.outputs.result }} + path: | + /home/ubuntu/pytest_workflow_*/*/.nextflow.log + /home/ubuntu/pytest_workflow_*/*/log.out + /home/ubuntu/pytest_workflow_*/*/log.err + /home/ubuntu/pytest_workflow_*/*/work + !/home/ubuntu/pytest_workflow_*/*/work/conda + !/home/ubuntu/pytest_workflow_*/*/work/singularity + !${{ github.workspace }}/.singularity + + confirm-pass: + runs-on: ubuntu-latest + needs: [pytest-changes, pytest] + if: always() + steps: + - name: All tests ok + if: ${{ success() || !contains(needs.*.result, 'failure') }} + run: exit 0 + - name: One or more tests failed + if: ${{ contains(needs.*.result, 'failure') }} + run: exit 1 + + - name: debug-print + if: always() + run: | + echo "toJSON(needs) = ${{ toJSON(needs) }}" + echo "toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}" diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml deleted file mode 100644 index 8be6d86d95d..00000000000 --- a/.github/workflows/test.yml +++ /dev/null @@ -1,778 +0,0 @@ -name: Run tests -on: - pull_request: - branches: [master] - merge_group: - types: [checks_requested] - branches: [master] - workflow_dispatch: - inputs: - runners: - description: "Runners to test on" - type: choice - options: - - "ubuntu-latest" - - "self-hosted" - default: "self-hosted" - -# Cancel if a newer run is started -concurrency: - group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} - cancel-in-progress: true - -env: - NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity - NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity - GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - -jobs: - pre-commit: - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4 - - uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5 - - uses: pre-commit/action@2c7b3805fd2a0fd8c1884dcaebf91fc102a13ecd # v3.0.1 - # FIXME Flip this off once we get to less than a couple hundred. Adding - # this so it will only run against changed files. It'll make it much - # easier to fix these as they come up rather than everything at once. - with: - extra_args: "--all-files" - - prettier: - runs-on: ubuntu-latest - steps: - - name: Check out repository - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4 - - - name: Install NodeJS - uses: actions/setup-node@0a44ba7841725637a19e28fa30b79a866c81b0a6 # v4 - with: - node-version: "20" - - - name: Install Prettier - run: npm install -g prettier@3.2.5 - - - name: Run Prettier --check - run: prettier --check . - - editorconfig: - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4 - - - uses: actions/setup-node@0a44ba7841725637a19e28fa30b79a866c81b0a6 # v4 - with: - node-version: "20" - - - name: Install editorconfig-checker - run: npm install -g editorconfig-checker - - - name: Run ECLint check - run: editorconfig-checker -exclude README.md $(git ls-files | grep -v test) - - pytest-changes: - name: pytest-changes - runs-on: ubuntu-latest - outputs: - tags: ${{ steps.filter.outputs.changes }} - modules: ${{ steps.tags.outputs.modules }} - subworkflows: ${{ steps.tags.outputs.subworkflows }} - steps: - - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4 - with: - fetch-depth: 2 # To retrieve the preceding commit. - - # TODO: change back to using dorny/paths-filter when https://github.com/dorny/paths-filter/pull/133 is implemented - - uses: mirpedrol/paths-filter@main - id: filter - with: - filters: "tests/config/pytest_modules.yml" - token: "" - - - name: Fetch module tags - id: tags - run: | - echo modules=$(echo '${{ steps.filter.outputs.changes }}' | jq -c '. | map(select(contains("modules"))) | map(gsub("modules/"; ""))') >> $GITHUB_OUTPUT - echo subworkflows=$(echo '${{ steps.filter.outputs.changes }}' | jq '. | map(select(contains("subworkflow"))) | map(gsub("subworkflows/"; ""))') >> $GITHUB_OUTPUT - - - name: debug - run: | - echo ${{ steps.tags.outputs.modules }} - echo ${{ steps.tags.outputs.subworkflows }} - - nf-test-changes: - name: nf-test-changes - runs-on: ubuntu-latest - outputs: - # Expose detected tags as 'modules' and 'workflows' output variables - paths: ${{ steps.list.outputs.components }} - modules: ${{ steps.outputs.outputs.modules }} - subworkflows: ${{ steps.outputs.outputs.subworkflows}} - # Prod for version bumping - - steps: - - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4 - with: - fetch-depth: 0 - - - name: List nf-test files - id: list - uses: adamrtalbot/detect-nf-test-changes@7c8be3ffd0d6538312b363c8c949dbbf5f26c3dd # v0.0.4 - with: - head: ${{ github.sha }} - base: ${{ github.event.pull_request.base.sha || github.event.merge_group.base_sha }} - n_parents: 2 - - - name: Separate modules and subworkflows - id: outputs - run: | - echo modules=$(echo '${{ steps.list.outputs.components }}' | jq -c '. | map(select(contains("modules"))) | map(gsub("modules/nf-core/"; ""))') >> $GITHUB_OUTPUT - echo subworkflows=$(echo '${{ steps.list.outputs.components }}' | jq '. | map(select(contains("subworkflows"))) | map(gsub("subworkflows/nf-core/"; ""))') >> $GITHUB_OUTPUT - - - name: debug - run: | - echo ${{ steps.outputs.outputs.modules }} - echo ${{ steps.outputs.outputs.subworkflows }} - - nf-core-lint-modules: - runs-on: ${{ github.event.inputs.runners || 'self-hosted' }} - name: nf-core-lint-modules - needs: [pytest-changes, nf-test-changes] - if: ${{ (needs.pytest-changes.outputs.modules != '[]') || ( needs.nf-test-changes.outputs.modules != '[]') }} - strategy: - fail-fast: false - matrix: - tags: - [ - "${{ fromJson(needs.pytest-changes.outputs.modules) }}", - "${{ fromJson(needs.nf-test-changes.outputs.modules) }}", - ] - steps: - - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4 - - - name: Set up Python - uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5 - with: - python-version: "3.11" - - - uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4 - id: cache-pip - with: - path: ~/.cache/pip - key: ${{ runner.os }}-pip - restore-keys: | - ${{ runner.os }}-pip - - - name: Install pip - run: python -m pip install --upgrade pip - - - uses: actions/setup-java@b36c23c0d998641eff861008f374ee103c25ac73 # v4 - with: - distribution: "temurin" - java-version: "17" - - - name: Setup Nextflow - uses: nf-core/setup-nextflow@v2 - - - name: Install nf-core tools development version - run: python -m pip install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git@dev - - - name: Lint module ${{ matrix.tags }} - run: nf-core modules lint ${{ matrix.tags }} - - nf-core-lint-subworkflows: - runs-on: ubuntu-latest - name: nf-core-lint-modules - needs: [pytest-changes, nf-test-changes] - if: ${{ (needs.pytest-changes.outputs.subworkflows != '[]') || ( needs.nf-test-changes.outputs.subworkflows != '[]') }} - strategy: - fail-fast: false - matrix: - tags: - [ - "${{ fromJson(needs.pytest-changes.outputs.subworkflows) }}", - "${{ fromJson(needs.nf-test-changes.outputs.subworkflows) }}", - ] - steps: - - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4 - - - name: Set up Python - uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5 - with: - python-version: "3.11" - - - name: Install pip - run: python -m pip install --upgrade pip - - - uses: actions/setup-java@b36c23c0d998641eff861008f374ee103c25ac73 # v4 - with: - distribution: "temurin" - java-version: "17" - - - name: Setup Nextflow - uses: nf-core/setup-nextflow@561fcfc7146dcb12e3871909b635ab092a781f34 # v2 - - - name: Install nf-core tools development version - run: python -m pip install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git@dev - - - name: Lint module ${{ matrix.tags }} - run: nf-core subworkflows lint ${{ matrix.tags }} - - pytest: - runs-on: ${{ github.event.inputs.runners || 'self-hosted' }} - name: pytest - needs: [pytest-changes] - if: needs.pytest-changes.outputs.tags != '[]' - strategy: - fail-fast: false - matrix: - tags: ["${{ fromJson(needs.pytest-changes.outputs.tags) }}"] - profile: [conda, docker, singularity] - exclude: - - tags: nf-test - - profile: conda - tags: backsub - - profile: conda - tags: bases2fastq - - profile: singularity - tags: bases2fastq - - profile: conda - tags: basicpy - - profile: conda - tags: bcl2fastq - - profile: conda - tags: bclconvert - - profile: conda - tags: bwa/aln - - profile: conda - tags: bwa/index - - profile: conda - tags: bwa/mem - - profile: conda - tags: bwa/sampe - - profile: conda - tags: bwa/samse - - profile: conda - tags: cellpose - - profile: conda - tags: cellrangerarc/count - - profile: conda - tags: cellrangerarc/mkfastq - - profile: conda - tags: cellrangerarc/mkref - - profile: conda - tags: cellrangeratac/count - - profile: conda - tags: cellrangeratac/mkfastq - - profile: conda - tags: cellrangeratac/mkref - - profile: conda - tags: checkm2/databasedownload - - profile: conda - tags: checkm2/predict - - profile: conda - tags: controlfreec/makegraph2 - - profile: conda - tags: coreograph - - profile: conda - tags: deepcell/mesmer - - profile: conda - tags: deepvariant - - profile: conda - tags: fastani - - profile: conda - tags: fastk/fastk - - profile: conda - tags: fastk/histex - - profile: conda - tags: fastk/merge - - profile: conda - tags: fcs/fcsadaptor - - profile: conda - tags: fcs/fcsgx - - profile: conda - tags: gatk4/cnnscorevariants - - profile: conda - tags: gatk4/determinegermlinecontigploidy - - profile: singularity - tags: gatk4/determinegermlinecontigploidy - - profile: conda - tags: gatk4/germlinecnvcaller - - profile: conda - tags: gatk4/postprocessgermlinecnvcalls - - profile: conda - tags: genescopefk - - profile: conda - tags: happy/sompy - - profile: conda - tags: hlala/preparegraph - - profile: conda - tags: ilastik/multicut - - profile: conda - tags: ilastik/pixelclassification - - profile: conda - tags: imputeme/vcftoprs - - profile: conda - tags: islandpath - - profile: conda - tags: manta/convertinversion - - profile: conda - tags: mcstaging/imc2mc - - profile: conda - tags: mcquant - - profile: conda - tags: medaka - - profile: conda - tags: merquryfk/katcomp - - profile: conda - tags: merquryfk/katgc - - profile: conda - tags: merquryfk/merquryfk - - profile: conda - tags: merquryfk/ploidyplot - - profile: conda - tags: minimap2/align - - profile: conda - tags: mitohifi/findmitoreference - - profile: conda - tags: mitohifi/mitohifi - - profile: conda - tags: nanoplot - - profile: conda - tags: ncbitools/vecscreen - - profile: conda - tags: parabricks/applybqsr - - profile: conda - tags: parabricks/dbsnp - - profile: conda - tags: parabricks/deepvariant - - profile: conda - tags: parabricks/fq2bam - - profile: conda - tags: parabricks/genotypegvcf - - profile: conda - tags: parabricks/haplotypecaller - - profile: conda - tags: parabricks/indexgvcf - - profile: conda - tags: parabricks/mutectcaller - - profile: conda - tags: picard/collecthsmetrics - - profile: conda - tags: picard/collectwgsmetrics - - profile: conda - tags: sentieon/applyvarcal - - profile: conda - tags: sentieon/datametrics - - profile: conda - tags: sentieon/dnamodelapply - - profile: conda - tags: sentieon/dnascope - - profile: conda - tags: sentieon/readwriter - - profile: conda - tags: sentieon/tnfilter - - profile: conda - tags: sentieon/tnhaplotyper2 - - profile: conda - tags: sentieon/tnscope - - profile: conda - tags: sentieon/varcal - - profile: conda - tags: sentieon/wgsmetrics - - profile: conda - tags: subworkflows/bam_qc_picard - - profile: conda - tags: subworkflows/bcl_demultiplex - - profile: conda - tags: subworkflows/fasta_clean_fcs - - profile: conda - tags: svanalyzer/svbenchmark - - profile: conda - tags: universc - - profile: singularity - tags: universc - - profile: conda - tags: vt/decompose - env: - NXF_ANSI_LOG: false - - steps: - - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4 - - - name: Set up Python - uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5 - with: - python-version: "3.11" - - - uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4 - id: cache-pip-pytest - with: - path: ~/.cache/pip - key: ${{ runner.os }}-pip-pytest - restore-keys: | - ${{ runner.os }}-pip-pytest - - - name: Install Python dependencies - run: python -m pip install --upgrade pip pytest-workflow cryptography - - - uses: actions/setup-java@b36c23c0d998641eff861008f374ee103c25ac73 # v4 - with: - distribution: "temurin" - java-version: "17" - - name: Setup Nextflow ${{ matrix.NXF_VER }} - uses: nf-core/setup-nextflow@v2 - with: - version: "${{ matrix.NXF_VER }}" - - - name: Setup apptainer - if: matrix.profile == 'singularity' - uses: eWaterCycle/setup-apptainer@main - - - name: Set up Singularity - if: matrix.profile == 'singularity' - run: | - mkdir -p $NXF_SINGULARITY_CACHEDIR - mkdir -p $NXF_SINGULARITY_LIBRARYDIR - - - name: Set up miniconda - uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3 - with: - miniconda-version: "latest" - channels: conda-forge,bioconda - python-version: ${{ matrix.python-version }} - - - name: Conda setup - run: | - conda clean -a - conda install -n base conda-libmamba-solver - conda config --set solver libmamba - echo $(realpath $CONDA)/condabin >> $GITHUB_PATH - echo $(realpath python) >> $GITHUB_PATH - - # Test the module - - name: Run pytest-workflow - # only use one thread for pytest-workflow to avoid race condition on conda cache. - run: TMPDIR=~ PROFILE=${{ matrix.profile }} pytest --tag ${{ matrix.tags }} --symlink --kwdof --git-aware --color=yes - - - name: Output log on failure - if: failure() - run: | - sudo apt-get update > /dev/null - sudo apt-get install bat > /dev/null - batcat --decorations=always --color=always /home/ubuntu/pytest_workflow_*/*/log.{out,err} - - - name: Setting global variables - uses: actions/github-script@60a0d83039c74a4aee543508d2ffcb1c3799cdea # v7 - id: parsed - with: - script: | - return '${{ matrix.tags }}'.toLowerCase().replaceAll(/\//g, '-').trim('-').trim('"') - result-encoding: string - - - name: Upload logs on failure - if: failure() - uses: actions/upload-artifact@50769540e7f4bd5e21e526ee35c689e35e0d6874 # v4 - with: - name: logs-${{ matrix.profile }}-${{ steps.parsed.outputs.result }} - path: | - /home/ubuntu/pytest_workflow_*/*/.nextflow.log - /home/ubuntu/pytest_workflow_*/*/log.out - /home/ubuntu/pytest_workflow_*/*/log.err - /home/ubuntu/pytest_workflow_*/*/work - !/home/ubuntu/pytest_workflow_*/*/work/conda - !/home/ubuntu/pytest_workflow_*/*/work/singularity - !${{ github.workspace }}/.singularity - - nf-test: - runs-on: ${{ github.event.inputs.runners || 'self-hosted' }} - name: nf-test - needs: [nf-test-changes] - if: ( needs.nf-test-changes.outputs.paths != '[]' ) - strategy: - fail-fast: false - matrix: - path: ["${{ fromJson(needs.nf-test-changes.outputs.paths) }}"] - profile: [conda, docker_self_hosted, singularity] - exclude: - - path: modules/nf-core/nf-test - - profile: conda - path: modules/nf-core/angsd/gl - - profile: conda - path: modules/nf-core/annotsv/installannotations - - profile: conda - path: modules/nf-core/happy/sompy - - profile: conda - path: modules/nf-core/backsub - - profile: conda - path: modules/nf-core/bakta/bakta - - profile: conda - path: modules/nf-core/bakta/baktadbdownload - - profile: conda - path: modules/nf-core/bases2fastq - - profile: conda - path: modules/nf-core/bcl2fastq - - profile: conda - path: modules/nf-core/bclconvert - - profile: conda - path: modules/nf-core/celesta - - profile: conda - path: modules/nf-core/cellpose - - profile: conda - path: modules/nf-core/cellranger/count - - profile: conda - path: modules/nf-core/cellranger/mkfastq - - profile: conda - path: modules/nf-core/cellranger/mkgtf - - profile: conda - path: modules/nf-core/cellranger/mkref - - profile: conda - path: modules/nf-core/cellranger/mkvdjref - - profile: conda - path: modules/nf-core/cellranger/multi - - profile: conda - path: modules/nf-core/cellranger/vdj - - profile: conda - path: modules/nf-core/checkqc - - profile: conda - path: modules/nf-core/custom/dumpsoftwareversions - - profile: conda - path: modules/nf-core/deepcell/mesmer - - profile: conda - path: modules/nf-core/deepvariant - - profile: conda - path: modules/nf-core/deepvariant/callvariants - - profile: conda - path: modules/nf-core/deepvariant/makeexamples - - profile: conda - path: modules/nf-core/deepvariant/postprocessvariants - - profile: conda - path: modules/nf-core/deepvariant/rundeepvariant - - profile: conda - path: modules/nf-core/ensemblvep/vep - - profile: conda - path: modules/nf-core/fastk/fastk - - profile: conda - path: modules/nf-core/cellrangerarc/mkgtf - - profile: conda - path: modules/nf-core/fastk/histex - - profile: conda - path: modules/nf-core/fastk/merge - - profile: conda - path: modules/nf-core/fcs/fcsadaptor - - profile: conda - path: modules/nf-core/fcs/fcsgx - - profile: conda - path: modules/nf-core/ganon/buildcustom - - profile: conda - path: modules/nf-core/ganon/classify - - profile: conda - path: modules/nf-core/ganon/report - - profile: conda - path: modules/nf-core/ganon/table - - profile: conda - path: modules/nf-core/gatk4/cnnscorevariants - - profile: conda - path: modules/nf-core/gatk4/determinegermlinecontigploidy - - profile: conda - path: modules/nf-core/genescopefk - - profile: conda - path: modules/nf-core/ilastik/multicut - - profile: conda - path: modules/nf-core/ilastik/pixelclassification - - profile: conda - path: modules/nf-core/imputeme/vcftoprs - - profile: conda - path: modules/nf-core/mcstaging/imc2mc - - profile: conda - path: modules/nf-core/mcquant - - profile: conda - path: modules/nf-core/mcstaging/phenoimager2mc - - profile: conda - path: modules/nf-core/merquryfk/katcomp - - profile: conda - path: modules/nf-core/merquryfk/katgc - - profile: conda - path: modules/nf-core/merquryfk/merquryfk - - profile: conda - path: modules/nf-core/merquryfk/ploidyplot - - profile: conda - path: modules/nf-core/molkartgarage/clahe - - profile: conda - path: modules/nf-core/quartonotebook - - profile: conda - path: modules/nf-core/scimap/spatiallda - - profile: conda - path: modules/nf-core/sentieon/bwaindex - - profile: conda - path: modules/nf-core/sentieon/bwamem - - profile: conda - path: modules/nf-core/sentieon/datametrics - - profile: conda - path: modules/nf-core/sentieon/dedup - - profile: conda - path: modules/nf-core/sentieon/qualcal - - profile: conda - path: modules/nf-core/spaceranger/mkgtf - - profile: conda - path: modules/nf-core/spaceranger/mkref - - profile: conda - path: modules/nf-core/spaceranger/count - - profile: conda - path: modules/nf-core/spotiflow - - profile: conda - path: modules/nf-core/svanalyzer/svbenchmark - - profile: conda - path: modules/nf-core/universc - - profile: singularity - path: modules/nf-core/universc - - profile: conda - path: modules/nf-core/vt/decompose - - profile: singularity - path: modules/nf-core/bases2fastq - - profile: conda - path: modules/nf-core/wittyer - - profile: conda - path: modules/nf-core/islandpath - - profile: conda - path: modules/nf-core/scimap/mcmicro - - profile: conda - path: subworkflows/nf-core/vcf_annotate_ensemblvep - - profile: conda - path: subworkflows/nf-core/bcl_demultiplex - - profile: conda - path: subworkflows/nf-core/deepvariant - - profile: conda - path: subworkflows/nf-core/fastq_align_bamcmp_bwa - - profile: conda - path: subworkflows/nf-core/fastq_align_bwa - env: - NXF_ANSI_LOG: false - NFTEST_VER: "0.9.0" - SENTIEON_LICENSE_MESSAGE: ${{ secrets.SENTIEON_LICENSE_MESSAGE }} - SENTIEON_ENCRYPTION_KEY: ${{ secrets.SENTIEON_ENCRYPTION_KEY }} - - steps: - - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4 - - - uses: actions/setup-java@b36c23c0d998641eff861008f374ee103c25ac73 # v4 - with: - distribution: "temurin" - java-version: "17" - - name: Setup Nextflow - uses: nf-core/setup-nextflow@v2 - - - name: Install nf-test - uses: nf-core/setup-nf-test@v1 - with: - version: ${{ env.NFTEST_VER }} - - - name: Setup apptainer - if: matrix.profile == 'singularity' - uses: eWaterCycle/setup-apptainer@main - - - name: Set up Singularity - if: matrix.profile == 'singularity' - run: | - mkdir -p $NXF_SINGULARITY_CACHEDIR - mkdir -p $NXF_SINGULARITY_LIBRARYDIR - - - name: Set up Python - uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5 - with: - python-version: "3.11" - - - uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4 - id: cache-pip-pdiff - with: - path: ~/.cache/pip - key: ${{ runner.os }}-pip-pdiff - restore-keys: | - ${{ runner.os }}-pip-pdiff - - - name: Install Python dependencies - run: python -m pip install --upgrade pip pdiff cryptography - - - name: Set up miniconda - if: matrix.profile == 'conda' - uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3 - with: - miniconda-version: "latest" - auto-update-conda: true - channels: conda-forge,bioconda - - - name: Conda setup - if: matrix.profile == 'conda' - run: | - conda clean -a - conda install -n base conda-libmamba-solver - conda config --set solver libmamba - echo $(realpath $CONDA)/condabin >> $GITHUB_PATH - echo $(realpath python) >> $GITHUB_PATH - - # Set up secrets - - name: Set up nextflow secrets - # TODO Only run if the tag includes `sentieon` - if: env.SENTIEON_ENCRYPTION_KEY != null && env.SENTIEON_LICENSE_MESSAGE != null - run: | - nextflow secrets set SENTIEON_AUTH_DATA $(python3 tests/modules/nf-core/sentieon/license_message.py encrypt --key "${{ secrets.SENTIEON_ENCRYPTION_KEY }}" --message "${{ secrets.SENTIEON_LICENSE_MESSAGE }}") - - # Test the module - - name: Run nf-test - env: - NFT_DIFF: "pdiff" - NFT_DIFF_ARGS: "--line-numbers --width 120 --expand-tabs=2" - SENTIEON_LICSRVR_IP: ${{ secrets.SENTIEON_LICSRVR_IP }} - SENTIEON_AUTH_MECH: "GitHub Actions - token" - run: | - # use "docker_self_hosted" if it runs on self-hosted runner and matrix.profile=docker - if [ "${{ matrix.profile }}" == "docker" ]; then - PROFILE="docker_self_hosted" - else - PROFILE=${{ matrix.profile }} - fi - - NFT_WORKDIR=~ \ - nf-test test \ - --profile=${{ matrix.profile }} \ - --tap=test.tap \ - --verbose \ - ${{ matrix.path }} - - - uses: pcolby/tap-summary@0959cbe1d4422e62afc65778cdaea6716c41d936 # v1 - with: - path: >- - test.tap - - - name: Clean up - if: always() - run: | - sudo rm -rf /home/ubuntu/tests/ - - confirm-pass: - runs-on: ubuntu-latest - needs: - [ - prettier, - editorconfig, - pytest-changes, - nf-core-lint-modules, - nf-core-lint-subworkflows, - pytest, - nf-test-changes, - nf-test, - ] - if: always() - steps: - - name: All tests ok - if: ${{ success() || !contains(needs.*.result, 'failure') }} - run: exit 0 - - name: One or more tests failed - if: ${{ contains(needs.*.result, 'failure') }} - run: exit 1 - - - name: debug-print - if: always() - run: | - echo "toJSON(needs) = ${{ toJSON(needs) }}" - echo "toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}" From 8897f68ce5a92b4890485fae0cdcdadc4e9d8be6 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Fri, 23 Aug 2024 11:22:04 -0500 Subject: [PATCH 02/30] ci: Add changed since, sharding, and ci --- .github/workflows/nf-test.yml | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml index 764c2295b66..97c2383a25c 100644 --- a/.github/workflows/nf-test.yml +++ b/.github/workflows/nf-test.yml @@ -1,4 +1,4 @@ -name: Run tests +name: Run nf-test on: pull_request: branches: [master] @@ -29,12 +29,10 @@ jobs: nf-test: runs-on: ${{ github.event.inputs.runners || 'self-hosted' }} name: nf-test - needs: [nf-test-changes] - if: ( needs.nf-test-changes.outputs.paths != '[]' ) strategy: fail-fast: false matrix: - path: ["${{ fromJson(needs.nf-test-changes.outputs.paths) }}"] + shard: [1, 2, 3] profile: [conda, docker_self_hosted, singularity] exclude: - path: modules/nf-core/nf-test @@ -171,6 +169,7 @@ jobs: env: NXF_ANSI_LOG: false NFTEST_VER: "0.9.0" + TOTAL_SHARDS: 3 SENTIEON_LICENSE_MESSAGE: ${{ secrets.SENTIEON_LICENSE_MESSAGE }} SENTIEON_ENCRYPTION_KEY: ${{ secrets.SENTIEON_ENCRYPTION_KEY }} @@ -238,7 +237,7 @@ jobs: nextflow secrets set SENTIEON_AUTH_DATA $(python3 tests/modules/nf-core/sentieon/license_message.py encrypt --key "${{ secrets.SENTIEON_ENCRYPTION_KEY }}" --message "${{ secrets.SENTIEON_LICENSE_MESSAGE }}") # Test the module - - name: Run nf-test + - name: Run Tests (Shard ${{ matrix.shard }}/${{ strategy.job-total }}) env: NFT_DIFF: "pdiff" NFT_DIFF_ARGS: "--line-numbers --width 120 --expand-tabs=2" @@ -256,8 +255,10 @@ jobs: nf-test test \ --profile=${{ matrix.profile }} \ --tap=test.tap \ + --ci \ --verbose \ - ${{ matrix.path }} + --changed-since HEAD^ \ + --shard ${{ matrix.shard }}/${{ env.TOTAL_SHARDS }} - uses: pcolby/tap-summary@0959cbe1d4422e62afc65778cdaea6716c41d936 # v1 with: From 2e20ff4d0cf30f472305b9184b7a84c958877907 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Fri, 23 Aug 2024 11:27:18 -0500 Subject: [PATCH 03/30] ci: Add filter to try to get jobs split up --- .github/workflows/nf-test.yml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml index 97c2383a25c..3fd89fc536b 100644 --- a/.github/workflows/nf-test.yml +++ b/.github/workflows/nf-test.yml @@ -34,6 +34,7 @@ jobs: matrix: shard: [1, 2, 3] profile: [conda, docker_self_hosted, singularity] + filter: [module, workflow] exclude: - path: modules/nf-core/nf-test - profile: conda @@ -258,7 +259,8 @@ jobs: --ci \ --verbose \ --changed-since HEAD^ \ - --shard ${{ matrix.shard }}/${{ env.TOTAL_SHARDS }} + --shard ${{ matrix.shard }}/${{ env.TOTAL_SHARDS }} \ + --filter ${{ matrix.filter }} - uses: pcolby/tap-summary@0959cbe1d4422e62afc65778cdaea6716c41d936 # v1 with: From ea0de231fccfc9c7beaaea27395df6e7d0873e9e Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Fri, 23 Aug 2024 11:27:54 -0500 Subject: [PATCH 04/30] ci: Switch to only-changed --- .github/workflows/nf-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml index 3fd89fc536b..d733aa9622d 100644 --- a/.github/workflows/nf-test.yml +++ b/.github/workflows/nf-test.yml @@ -258,7 +258,7 @@ jobs: --tap=test.tap \ --ci \ --verbose \ - --changed-since HEAD^ \ + --only-changed \ --shard ${{ matrix.shard }}/${{ env.TOTAL_SHARDS }} \ --filter ${{ matrix.filter }} From 2c5b4bd0a0c361ad44599414cace8ec41ea65513 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Fri, 23 Aug 2024 11:29:19 -0500 Subject: [PATCH 05/30] ci: See if follow-dependencies works without "related-tests" --- .github/workflows/nf-test.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml index d733aa9622d..091d33af97f 100644 --- a/.github/workflows/nf-test.yml +++ b/.github/workflows/nf-test.yml @@ -260,7 +260,8 @@ jobs: --verbose \ --only-changed \ --shard ${{ matrix.shard }}/${{ env.TOTAL_SHARDS }} \ - --filter ${{ matrix.filter }} + --filter ${{ matrix.filter }} \ + --follow-dependencies - uses: pcolby/tap-summary@0959cbe1d4422e62afc65778cdaea6716c41d936 # v1 with: From 6322086e54dd63ed8328cc0d7234010babd212f0 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Fri, 23 Aug 2024 11:40:01 -0500 Subject: [PATCH 06/30] ci: Remove skipped tests Idk what we're going to do about these... --- .github/workflows/nf-test.yml | 265 +++++++++++++++++----------------- 1 file changed, 133 insertions(+), 132 deletions(-) diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml index 091d33af97f..c1856e0189b 100644 --- a/.github/workflows/nf-test.yml +++ b/.github/workflows/nf-test.yml @@ -35,138 +35,6 @@ jobs: shard: [1, 2, 3] profile: [conda, docker_self_hosted, singularity] filter: [module, workflow] - exclude: - - path: modules/nf-core/nf-test - - profile: conda - path: modules/nf-core/angsd/gl - - profile: conda - path: modules/nf-core/annotsv/installannotations - - profile: conda - path: modules/nf-core/happy/sompy - - profile: conda - path: modules/nf-core/backsub - - profile: conda - path: modules/nf-core/bakta/bakta - - profile: conda - path: modules/nf-core/bakta/baktadbdownload - - profile: conda - path: modules/nf-core/bases2fastq - - profile: conda - path: modules/nf-core/bcl2fastq - - profile: conda - path: modules/nf-core/bclconvert - - profile: conda - path: modules/nf-core/celesta - - profile: conda - path: modules/nf-core/cellpose - - profile: conda - path: modules/nf-core/cellranger/count - - profile: conda - path: modules/nf-core/cellranger/mkfastq - - profile: conda - path: modules/nf-core/cellranger/mkgtf - - profile: conda - path: modules/nf-core/cellranger/mkref - - profile: conda - path: modules/nf-core/cellranger/mkvdjref - - profile: conda - path: modules/nf-core/cellranger/multi - - profile: conda - path: modules/nf-core/cellranger/vdj - - profile: conda - path: modules/nf-core/checkqc - - profile: conda - path: modules/nf-core/custom/dumpsoftwareversions - - profile: conda - path: modules/nf-core/deepcell/mesmer - - profile: conda - path: modules/nf-core/deepvariant - - profile: conda - path: modules/nf-core/ensemblvep/vep - - profile: conda - path: modules/nf-core/fastk/fastk - - profile: conda - path: modules/nf-core/fastk/histex - - profile: conda - path: modules/nf-core/fastk/merge - - profile: conda - path: modules/nf-core/fcs/fcsadaptor - - profile: conda - path: modules/nf-core/fcs/fcsgx - - profile: conda - path: modules/nf-core/ganon/buildcustom - - profile: conda - path: modules/nf-core/ganon/classify - - profile: conda - path: modules/nf-core/ganon/report - - profile: conda - path: modules/nf-core/ganon/table - - profile: conda - path: modules/nf-core/gatk4/cnnscorevariants - - profile: conda - path: modules/nf-core/gatk4/determinegermlinecontigploidy - - profile: conda - path: modules/nf-core/genescopefk - - profile: conda - path: modules/nf-core/ilastik/multicut - - profile: conda - path: modules/nf-core/ilastik/pixelclassification - - profile: conda - path: modules/nf-core/imputeme/vcftoprs - - profile: conda - path: modules/nf-core/mcquant - - profile: conda - path: modules/nf-core/merquryfk/katcomp - - profile: conda - path: modules/nf-core/merquryfk/katgc - - profile: conda - path: modules/nf-core/merquryfk/merquryfk - - profile: conda - path: modules/nf-core/merquryfk/ploidyplot - - profile: conda - path: modules/nf-core/molkartgarage/clahe - - profile: conda - path: modules/nf-core/quartonotebook - - profile: conda - path: modules/nf-core/scimap/spatiallda - - profile: conda - path: modules/nf-core/sentieon/bwaindex - - profile: conda - path: modules/nf-core/sentieon/bwamem - - profile: conda - path: modules/nf-core/sentieon/dedup - - profile: conda - path: modules/nf-core/sentieon/qualcal - - profile: conda - path: modules/nf-core/spaceranger/mkgtf - - profile: conda - path: modules/nf-core/spaceranger/mkref - - profile: conda - path: modules/nf-core/spaceranger/count - - profile: conda - path: modules/nf-core/spotiflow - - profile: conda - path: modules/nf-core/svanalyzer/svbenchmark - - profile: conda - path: modules/nf-core/universc - - profile: singularity - path: modules/nf-core/universc - - profile: conda - path: modules/nf-core/vt/decompose - - profile: singularity - path: modules/nf-core/bases2fastq - - profile: conda - path: modules/nf-core/wittyer - - profile: conda - path: modules/nf-core/islandpath - - profile: conda - path: subworkflows/nf-core/vcf_annotate_ensemblvep - - profile: conda - path: subworkflows/nf-core/bcl_demultiplex - - profile: conda - path: subworkflows/nf-core/fastq_align_bamcmp_bwa - - profile: conda - path: subworkflows/nf-core/fastq_align_bwa env: NXF_ANSI_LOG: false NFTEST_VER: "0.9.0" @@ -272,3 +140,136 @@ jobs: if: always() run: | sudo rm -rf /home/ubuntu/tests/ + +# TODO What do we do with these? +# - path: modules/nf-core/nf-test +# - profile: conda +# path: modules/nf-core/angsd/gl +# - profile: conda +# path: modules/nf-core/annotsv/installannotations +# - profile: conda +# path: modules/nf-core/happy/sompy +# - profile: conda +# path: modules/nf-core/backsub +# - profile: conda +# path: modules/nf-core/bakta/bakta +# - profile: conda +# path: modules/nf-core/bakta/baktadbdownload +# - profile: conda +# path: modules/nf-core/bases2fastq +# - profile: conda +# path: modules/nf-core/bcl2fastq +# - profile: conda +# path: modules/nf-core/bclconvert +# - profile: conda +# path: modules/nf-core/celesta +# - profile: conda +# path: modules/nf-core/cellpose +# - profile: conda +# path: modules/nf-core/cellranger/count +# - profile: conda +# path: modules/nf-core/cellranger/mkfastq +# - profile: conda +# path: modules/nf-core/cellranger/mkgtf +# - profile: conda +# path: modules/nf-core/cellranger/mkref +# - profile: conda +# path: modules/nf-core/cellranger/mkvdjref +# - profile: conda +# path: modules/nf-core/cellranger/multi +# - profile: conda +# path: modules/nf-core/cellranger/vdj +# - profile: conda +# path: modules/nf-core/checkqc +# - profile: conda +# path: modules/nf-core/custom/dumpsoftwareversions +# - profile: conda +# path: modules/nf-core/deepcell/mesmer +# - profile: conda +# path: modules/nf-core/deepvariant +# - profile: conda +# path: modules/nf-core/ensemblvep/vep +# - profile: conda +# path: modules/nf-core/fastk/fastk +# - profile: conda +# path: modules/nf-core/fastk/histex +# - profile: conda +# path: modules/nf-core/fastk/merge +# - profile: conda +# path: modules/nf-core/fcs/fcsadaptor +# - profile: conda +# path: modules/nf-core/fcs/fcsgx +# - profile: conda +# path: modules/nf-core/ganon/buildcustom +# - profile: conda +# path: modules/nf-core/ganon/classify +# - profile: conda +# path: modules/nf-core/ganon/report +# - profile: conda +# path: modules/nf-core/ganon/table +# - profile: conda +# path: modules/nf-core/gatk4/cnnscorevariants +# - profile: conda +# path: modules/nf-core/gatk4/determinegermlinecontigploidy +# - profile: conda +# path: modules/nf-core/genescopefk +# - profile: conda +# path: modules/nf-core/ilastik/multicut +# - profile: conda +# path: modules/nf-core/ilastik/pixelclassification +# - profile: conda +# path: modules/nf-core/imputeme/vcftoprs +# - profile: conda +# path: modules/nf-core/mcquant +# - profile: conda +# path: modules/nf-core/merquryfk/katcomp +# - profile: conda +# path: modules/nf-core/merquryfk/katgc +# - profile: conda +# path: modules/nf-core/merquryfk/merquryfk +# - profile: conda +# path: modules/nf-core/merquryfk/ploidyplot +# - profile: conda +# path: modules/nf-core/molkartgarage/clahe +# - profile: conda +# path: modules/nf-core/quartonotebook +# - profile: conda +# path: modules/nf-core/scimap/spatiallda +# - profile: conda +# path: modules/nf-core/sentieon/bwaindex +# - profile: conda +# path: modules/nf-core/sentieon/bwamem +# - profile: conda +# path: modules/nf-core/sentieon/dedup +# - profile: conda +# path: modules/nf-core/sentieon/qualcal +# - profile: conda +# path: modules/nf-core/spaceranger/mkgtf +# - profile: conda +# path: modules/nf-core/spaceranger/mkref +# - profile: conda +# path: modules/nf-core/spaceranger/count +# - profile: conda +# path: modules/nf-core/spotiflow +# - profile: conda +# path: modules/nf-core/svanalyzer/svbenchmark +# - profile: conda +# path: modules/nf-core/universc +# - profile: singularity +# path: modules/nf-core/universc +# - profile: conda +# path: modules/nf-core/vt/decompose +# - profile: singularity +# path: modules/nf-core/bases2fastq +# - profile: conda +# path: modules/nf-core/wittyer +# - profile: conda +# path: modules/nf-core/islandpath +# - profile: conda +# path: subworkflows/nf-core/vcf_annotate_ensemblvep +# - profile: conda +# path: subworkflows/nf-core/bcl_demultiplex +# - profile: conda +# path: subworkflows/nf-core/fastq_align_bamcmp_bwa +# - profile: conda +# path: subworkflows/nf-core/fastq_align_bwa From 71d9e5aa851447e375d6a33dd8663aece932cb47 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Fri, 23 Aug 2024 11:49:32 -0500 Subject: [PATCH 07/30] ci: Actually use the nf-test version --- .github/workflows/nf-test.yml | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml index c1856e0189b..57f3604c316 100644 --- a/.github/workflows/nf-test.yml +++ b/.github/workflows/nf-test.yml @@ -37,6 +37,7 @@ jobs: filter: [module, workflow] env: NXF_ANSI_LOG: false + NXF_VER: "24.04.4" NFTEST_VER: "0.9.0" TOTAL_SHARDS: 3 SENTIEON_LICENSE_MESSAGE: ${{ secrets.SENTIEON_LICENSE_MESSAGE }} @@ -51,9 +52,13 @@ jobs: java-version: "17" - name: Setup Nextflow uses: nf-core/setup-nextflow@v2 + with: + version: ${{ env.NXF_VER }} - name: Install nf-test uses: nf-core/setup-nf-test@v1 + with: + version: ${{ env.NFTEST_VER }} - name: Setup apptainer if: matrix.profile == 'singularity' From afd049de7ff8cf8be963065a8cd8ffec9580eb0f Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Fri, 23 Aug 2024 11:56:14 -0500 Subject: [PATCH 08/30] ci: module => process --- .github/workflows/nf-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml index 57f3604c316..1150a8c53e0 100644 --- a/.github/workflows/nf-test.yml +++ b/.github/workflows/nf-test.yml @@ -34,7 +34,7 @@ jobs: matrix: shard: [1, 2, 3] profile: [conda, docker_self_hosted, singularity] - filter: [module, workflow] + filter: [process, workflow] env: NXF_ANSI_LOG: false NXF_VER: "24.04.4" From a823ee379cc2a49da63c2bd748ef8f3fef8bd53d Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Fri, 23 Aug 2024 12:04:37 -0500 Subject: [PATCH 09/30] ci: Clean up job names --- .github/workflows/nf-test.yml | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml index 1150a8c53e0..c0ebe3af253 100644 --- a/.github/workflows/nf-test.yml +++ b/.github/workflows/nf-test.yml @@ -27,8 +27,8 @@ env: jobs: nf-test: - runs-on: ${{ github.event.inputs.runners || 'self-hosted' }} - name: nf-test + runs-on: ${{ github.event.inputs.runners || 'self-hosted' }} + name: ${{ matrix.profile }}\|${{ matrix.filter }}\|Shard ${{ matrix.shard }} strategy: fail-fast: false matrix: @@ -111,7 +111,7 @@ jobs: nextflow secrets set SENTIEON_AUTH_DATA $(python3 tests/modules/nf-core/sentieon/license_message.py encrypt --key "${{ secrets.SENTIEON_ENCRYPTION_KEY }}" --message "${{ secrets.SENTIEON_LICENSE_MESSAGE }}") # Test the module - - name: Run Tests (Shard ${{ matrix.shard }}/${{ strategy.job-total }}) + - name: Run Tests (Shard ${{ matrix.shard }}/${{ env.TOTAL_SHARDS }}) env: NFT_DIFF: "pdiff" NFT_DIFF_ARGS: "--line-numbers --width 120 --expand-tabs=2" @@ -136,6 +136,8 @@ jobs: --filter ${{ matrix.filter }} \ --follow-dependencies + # TODO If no test.tap, then make one to spoof? + - uses: pcolby/tap-summary@0959cbe1d4422e62afc65778cdaea6716c41d936 # v1 with: path: >- @@ -147,6 +149,7 @@ jobs: sudo rm -rf /home/ubuntu/tests/ # TODO What do we do with these? +# I think we can require Docker,modules,Shard 1..Singularity,subworkflows,3 and skip the condas now # - path: modules/nf-core/nf-test # - profile: conda # path: modules/nf-core/angsd/gl From 0d2c26c9da948dce3a5cffcb9c1eddf04beb3266 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Fri, 23 Aug 2024 12:06:31 -0500 Subject: [PATCH 10/30] dummy: Make a change --- modules/nf-core/bowtie/align/main.nf | 1 + 1 file changed, 1 insertion(+) diff --git a/modules/nf-core/bowtie/align/main.nf b/modules/nf-core/bowtie/align/main.nf index 5e72b02a678..42939e51586 100644 --- a/modules/nf-core/bowtie/align/main.nf +++ b/modules/nf-core/bowtie/align/main.nf @@ -29,6 +29,7 @@ process BOWTIE_ALIGN { def endedness = meta.single_end ? "$reads" : "-1 ${reads[0]} -2 ${reads[1]}" """ INDEX=\$(find -L ./ -name "*.3.ebwt" | sed 's/\\.3.ebwt\$//') + bowtie \\ --threads $task.cpus \\ --sam \\ From 97f64066ff1834bd441c6dd71881613948543677 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Fri, 23 Aug 2024 12:11:20 -0500 Subject: [PATCH 11/30] ci: Skip test.tap --- .github/workflows/nf-test.yml | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml index c0ebe3af253..5b9ba302f01 100644 --- a/.github/workflows/nf-test.yml +++ b/.github/workflows/nf-test.yml @@ -136,12 +136,11 @@ jobs: --filter ${{ matrix.filter }} \ --follow-dependencies - # TODO If no test.tap, then make one to spoof? - - - uses: pcolby/tap-summary@0959cbe1d4422e62afc65778cdaea6716c41d936 # v1 - with: - path: >- - test.tap + # TODO If no test.tap, then make one to spoof? + # - uses: pcolby/tap-summary@0959cbe1d4422e62afc65778cdaea6716c41d936 # v1 + # with: + # path: >- + # test.tap - name: Clean up if: always() From c486922ad5573c8e7e03412c1cc9a868b85d48da Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Fri, 23 Aug 2024 12:12:30 -0500 Subject: [PATCH 12/30] ci: Add fetch-depth --- .github/workflows/nf-test.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml index 5b9ba302f01..38aeae2974c 100644 --- a/.github/workflows/nf-test.yml +++ b/.github/workflows/nf-test.yml @@ -45,6 +45,8 @@ jobs: steps: - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4 + with: + fetch-depth: 0 - uses: actions/setup-java@b36c23c0d998641eff861008f374ee103c25ac73 # v4 with: From d58ecdbfd35a3612f24a7af436aac3563f546774 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Fri, 23 Aug 2024 12:29:30 -0500 Subject: [PATCH 13/30] ci: Clean up name --- .github/workflows/nf-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml index 38aeae2974c..065a16108dd 100644 --- a/.github/workflows/nf-test.yml +++ b/.github/workflows/nf-test.yml @@ -28,7 +28,7 @@ env: jobs: nf-test: runs-on: ${{ github.event.inputs.runners || 'self-hosted' }} - name: ${{ matrix.profile }}\|${{ matrix.filter }}\|Shard ${{ matrix.shard }} + name: ${{ matrix.profile }}|${{ matrix.filter }}|${{ matrix.shard }} strategy: fail-fast: false matrix: From 52a826d329ad890ba8808f08d58dab3ed92f0281 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Fri, 23 Aug 2024 12:36:20 -0500 Subject: [PATCH 14/30] ci: Lint everything --- .github/workflows/lint.yml | 32 +++++---------------------- .github/workflows/pytest-workflow.yml | 2 +- 2 files changed, 7 insertions(+), 27 deletions(-) diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml index 185916f517d..38e7f4e1721 100644 --- a/.github/workflows/lint.yml +++ b/.github/workflows/lint.yml @@ -70,20 +70,11 @@ jobs: - name: Run ECLint check run: editorconfig-checker -exclude README.md $(git ls-files | grep -v test) - # FIXME Lint everything? nf-core-lint-modules: runs-on: ${{ github.event.inputs.runners || 'self-hosted' }} - name: nf-core-lint-modules - needs: [pytest-changes, nf-test-changes] - if: ${{ (needs.pytest-changes.outputs.modules != '[]') || ( needs.nf-test-changes.outputs.modules != '[]') }} + name: nf-core lint modules strategy: fail-fast: false - matrix: - tags: - [ - "${{ fromJson(needs.pytest-changes.outputs.modules) }}", - "${{ fromJson(needs.nf-test-changes.outputs.modules) }}", - ] steps: - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4 @@ -114,23 +105,12 @@ jobs: - name: Install nf-core tools development version run: python -m pip install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git@dev - - name: Lint module ${{ matrix.tags }} - run: nf-core modules lint ${{ matrix.tags }} + - name: Lint modules + run: nf-core modules lint -a - # FIXME Lint everything? nf-core-lint-subworkflows: runs-on: ubuntu-latest - name: nf-core-lint-modules - needs: [pytest-changes, nf-test-changes] - if: ${{ (needs.pytest-changes.outputs.subworkflows != '[]') || ( needs.nf-test-changes.outputs.subworkflows != '[]') }} - strategy: - fail-fast: false - matrix: - tags: - [ - "${{ fromJson(needs.pytest-changes.outputs.subworkflows) }}", - "${{ fromJson(needs.nf-test-changes.outputs.subworkflows) }}", - ] + name: nf-core lint subworkflows steps: - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4 @@ -153,5 +133,5 @@ jobs: - name: Install nf-core tools development version run: python -m pip install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git@dev - - name: Lint module ${{ matrix.tags }} - run: nf-core subworkflows lint ${{ matrix.tags }} + - name: Lint subworkflows + run: nf-core subworkflows lint -a diff --git a/.github/workflows/pytest-workflow.yml b/.github/workflows/pytest-workflow.yml index 23522d5529b..de04a1570a8 100644 --- a/.github/workflows/pytest-workflow.yml +++ b/.github/workflows/pytest-workflow.yml @@ -1,4 +1,4 @@ -name: Run tests +name: Run pytest-workflow on: pull_request: branches: [master] From 1043d64b38f6a5253cc40754f5ca1ea83d7ce4a7 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Fri, 23 Aug 2024 12:42:15 -0500 Subject: [PATCH 15/30] ci: Get the job names clean --- .github/workflows/nf-test.yml | 13 ++++++++++--- 1 file changed, 10 insertions(+), 3 deletions(-) diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml index 065a16108dd..4a87534aaed 100644 --- a/.github/workflows/nf-test.yml +++ b/.github/workflows/nf-test.yml @@ -28,13 +28,20 @@ env: jobs: nf-test: runs-on: ${{ github.event.inputs.runners || 'self-hosted' }} - name: ${{ matrix.profile }}|${{ matrix.filter }}|${{ matrix.shard }} + # NOTE I think this is the cleanest way to get them organized + # process | conda | 1 + # process | conda | 2 + # process | conda | 3 + # process | docker_self_hosted | 1 + # ... + # workflow | singularity | 3 + name: ${{ matrix.filter }} | ${{ matrix.profile }} | ${{ matrix.shard }} strategy: fail-fast: false matrix: - shard: [1, 2, 3] - profile: [conda, docker_self_hosted, singularity] filter: [process, workflow] + profile: [conda, docker_self_hosted, singularity] + shard: [1, 2, 3] env: NXF_ANSI_LOG: false NXF_VER: "24.04.4" From 94c245387efd0d7d4cea6e91b09ed2f13186f94c Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Fri, 23 Aug 2024 14:16:16 -0500 Subject: [PATCH 16/30] ci: Add hide-progress on linting --- .github/workflows/lint.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml index 38e7f4e1721..d9e8215f3e7 100644 --- a/.github/workflows/lint.yml +++ b/.github/workflows/lint.yml @@ -106,7 +106,7 @@ jobs: run: python -m pip install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git@dev - name: Lint modules - run: nf-core modules lint -a + run: nf-core --hide-progress modules lint -a nf-core-lint-subworkflows: runs-on: ubuntu-latest @@ -134,4 +134,4 @@ jobs: run: python -m pip install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git@dev - name: Lint subworkflows - run: nf-core subworkflows lint -a + run: nf-core --hide-progress subworkflows lint -a From ab5194b3476f7a5dafb90cd4836b03710fa6e306 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Sat, 24 Aug 2024 17:19:01 -0500 Subject: [PATCH 17/30] ci: Add psuedocode for conda-fail.yml https://nfcore.slack.com/archives/CJRH30T6V/p1724406283145319 --- .github/workflows/nf-test.yml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml index 4a87534aaed..69d95b7d2e0 100644 --- a/.github/workflows/nf-test.yml +++ b/.github/workflows/nf-test.yml @@ -51,6 +51,8 @@ jobs: SENTIEON_ENCRYPTION_KEY: ${{ secrets.SENTIEON_ENCRYPTION_KEY }} steps: + # TODO If conda-fail.yml exists and matrix = conda skip + - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4 with: fetch-depth: 0 @@ -145,6 +147,8 @@ jobs: --filter ${{ matrix.filter }} \ --follow-dependencies + # TODO If matrix == conda create a conda-fail.yml and commit it + # TODO If no test.tap, then make one to spoof? # - uses: pcolby/tap-summary@0959cbe1d4422e62afc65778cdaea6716c41d936 # v1 # with: From 2a218e3da33ae9647fdb0fe078fc0e4f85e3c9ef Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Tue, 10 Sep 2024 11:49:33 -0500 Subject: [PATCH 18/30] test: Snapshot the versions contents, not the hash https://github.com/nf-core/modules/issues/6505 --- modules/nf-core/bowtie/build/tests/main.nf.test | 4 +++- .../nf-core/bowtie/build/tests/main.nf.test.snap | 14 ++++++++++++++ 2 files changed, 17 insertions(+), 1 deletion(-) diff --git a/modules/nf-core/bowtie/build/tests/main.nf.test b/modules/nf-core/bowtie/build/tests/main.nf.test index 25fb3dad83b..b58f1d69a2f 100644 --- a/modules/nf-core/bowtie/build/tests/main.nf.test +++ b/modules/nf-core/bowtie/build/tests/main.nf.test @@ -34,6 +34,7 @@ nextflow_process { test("sarscov2 - fasta - stub") { options "-stub" + tag "version" when { process { @@ -48,7 +49,8 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(process.out).match() }, + { assert snapshot(path(process.out.versions.get(0)).yaml).match("versions") }, ) } diff --git a/modules/nf-core/bowtie/build/tests/main.nf.test.snap b/modules/nf-core/bowtie/build/tests/main.nf.test.snap index e8061756ba2..6951ac5b5d4 100644 --- a/modules/nf-core/bowtie/build/tests/main.nf.test.snap +++ b/modules/nf-core/bowtie/build/tests/main.nf.test.snap @@ -46,6 +46,20 @@ }, "timestamp": "2024-06-18T08:38:14.852528155" }, + "versions": { + "content": [ + { + "BOWTIE_BUILD": { + "bowtie": "1.3.0" + } + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-10T11:48:00.007395903" + }, "sarscov2 - fasta": { "content": [ { From e833cd5b6057a66c3258f8c9d787ba411916534d Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Wed, 18 Sep 2024 13:35:34 -0500 Subject: [PATCH 19/30] ci: Keep running nf-core lint the way it was Blocked by https://github.com/nf-core/tools/issues/3140 --- .github/workflows/lint.yml | 55 +++++++++++++++++++++++++++++++++----- 1 file changed, 49 insertions(+), 6 deletions(-) diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml index d9e8215f3e7..bb20af0f209 100644 --- a/.github/workflows/lint.yml +++ b/.github/workflows/lint.yml @@ -70,16 +70,53 @@ jobs: - name: Run ECLint check run: editorconfig-checker -exclude README.md $(git ls-files | grep -v test) + ################### + # nf-core linting # + ################### + nf-core-changes: + name: nf-core-changes + runs-on: ubuntu-latest + outputs: + tags: ${{ steps.filter.outputs.changes }} + modules: ${{ steps.tags.outputs.modules }} + subworkflows: ${{ steps.tags.outputs.subworkflows }} + steps: + - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4 + with: + fetch-depth: 2 # To retrieve the preceding commit. + + # TODO: change back to using dorny/paths-filter when https://github.com/dorny/paths-filter/pull/133 is implemented + - uses: mirpedrol/paths-filter@main + id: filter + with: + filters: "tests/config/pytest_modules.yml" + token: "" + + - name: Fetch module tags + id: tags + run: | + echo modules=$(echo '${{ steps.filter.outputs.changes }}' | jq -c '. | map(select(contains("modules"))) | map(gsub("modules/"; ""))') >> $GITHUB_OUTPUT + echo subworkflows=$(echo '${{ steps.filter.outputs.changes }}' | jq '. | map(select(contains("subworkflow"))) | map(gsub("subworkflows/"; ""))') >> $GITHUB_OUTPUT + + - name: debug + run: | + echo ${{ steps.tags.outputs.modules }} + echo ${{ steps.tags.outputs.subworkflows }} + nf-core-lint-modules: runs-on: ${{ github.event.inputs.runners || 'self-hosted' }} name: nf-core lint modules + needs: nf-core-changes + if: ${{ (needs.nf-core-changes.outputs.modules != '[]') }} strategy: fail-fast: false + matrix: + tags: "${{ fromJson(needs.nf-core-changes.outputs.modules) }}" steps: - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4 - name: Set up Python - uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f # v5 + uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5 with: python-version: "3.11" @@ -105,17 +142,23 @@ jobs: - name: Install nf-core tools development version run: python -m pip install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git@dev - - name: Lint modules - run: nf-core --hide-progress modules lint -a + - name: Lint module ${{ matrix.tags }} + run: nf-core modules lint ${{ matrix.tags }} nf-core-lint-subworkflows: runs-on: ubuntu-latest name: nf-core lint subworkflows + needs: nf-core-changes + if: ${{ (needs.nf-core-changes.outputs.subworkflows != '[]') }} + strategy: + fail-fast: false + matrix: + tags: "${{ fromJson(needs.nf-core-changes.outputs.subworkflows) }}" steps: - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4 - name: Set up Python - uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f # v5 + uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5 with: python-version: "3.11" @@ -133,5 +176,5 @@ jobs: - name: Install nf-core tools development version run: python -m pip install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git@dev - - name: Lint subworkflows - run: nf-core --hide-progress subworkflows lint -a + - name: Lint module ${{ matrix.tags }} + run: nf-core subworkflows lint ${{ matrix.tags }} From 392ffe78e4a2ea42ade220cf0d611799c5275797 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Tue, 24 Sep 2024 07:26:18 -0500 Subject: [PATCH 20/30] ci: Move conda skips out --- .github/conda_skip.yml | 133 +++++++++++++++++++++++++++++++++ .github/workflows/nf-test.yml | 134 ---------------------------------- 2 files changed, 133 insertions(+), 134 deletions(-) create mode 100644 .github/conda_skip.yml diff --git a/.github/conda_skip.yml b/.github/conda_skip.yml new file mode 100644 index 00000000000..44e43a740a4 --- /dev/null +++ b/.github/conda_skip.yml @@ -0,0 +1,133 @@ +# TODO What do we do with these? +# I think we can require Docker,modules,Shard 1..Singularity,subworkflows,3 and skip the condas now +# - path: modules/nf-core/nf-test +# - profile: conda +# path: modules/nf-core/angsd/gl +# - profile: conda +# path: modules/nf-core/annotsv/installannotations +# - profile: conda +# path: modules/nf-core/happy/sompy +# - profile: conda +# path: modules/nf-core/backsub +# - profile: conda +# path: modules/nf-core/bakta/bakta +# - profile: conda +# path: modules/nf-core/bakta/baktadbdownload +# - profile: conda +# path: modules/nf-core/bases2fastq +# - profile: conda +# path: modules/nf-core/bcl2fastq +# - profile: conda +# path: modules/nf-core/bclconvert +# - profile: conda +# path: modules/nf-core/celesta +# - profile: conda +# path: modules/nf-core/cellpose +# - profile: conda +# path: modules/nf-core/cellranger/count +# - profile: conda +# path: modules/nf-core/cellranger/mkfastq +# - profile: conda +# path: modules/nf-core/cellranger/mkgtf +# - profile: conda +# path: modules/nf-core/cellranger/mkref +# - profile: conda +# path: modules/nf-core/cellranger/mkvdjref +# - profile: conda +# path: modules/nf-core/cellranger/multi +# - profile: conda +# path: modules/nf-core/cellranger/vdj +# - profile: conda +# path: modules/nf-core/checkqc +# - profile: conda +# path: modules/nf-core/custom/dumpsoftwareversions +# - profile: conda +# path: modules/nf-core/deepcell/mesmer +# - profile: conda +# path: modules/nf-core/deepvariant +# - profile: conda +# path: modules/nf-core/ensemblvep/vep +# - profile: conda +# path: modules/nf-core/fastk/fastk +# - profile: conda +# path: modules/nf-core/fastk/histex +# - profile: conda +# path: modules/nf-core/fastk/merge +# - profile: conda +# path: modules/nf-core/fcs/fcsadaptor +# - profile: conda +# path: modules/nf-core/fcs/fcsgx +# - profile: conda +# path: modules/nf-core/ganon/buildcustom +# - profile: conda +# path: modules/nf-core/ganon/classify +# - profile: conda +# path: modules/nf-core/ganon/report +# - profile: conda +# path: modules/nf-core/ganon/table +# - profile: conda +# path: modules/nf-core/gatk4/cnnscorevariants +# - profile: conda +# path: modules/nf-core/gatk4/determinegermlinecontigploidy +# - profile: conda +# path: modules/nf-core/genescopefk +# - profile: conda +# path: modules/nf-core/ilastik/multicut +# - profile: conda +# path: modules/nf-core/ilastik/pixelclassification +# - profile: conda +# path: modules/nf-core/imputeme/vcftoprs +# - profile: conda +# path: modules/nf-core/mcquant +# - profile: conda +# path: modules/nf-core/merquryfk/katcomp +# - profile: conda +# path: modules/nf-core/merquryfk/katgc +# - profile: conda +# path: modules/nf-core/merquryfk/merquryfk +# - profile: conda +# path: modules/nf-core/merquryfk/ploidyplot +# - profile: conda +# path: modules/nf-core/molkartgarage/clahe +# - profile: conda +# path: modules/nf-core/quartonotebook +# - profile: conda +# path: modules/nf-core/scimap/spatiallda +# - profile: conda +# path: modules/nf-core/sentieon/bwaindex +# - profile: conda +# path: modules/nf-core/sentieon/bwamem +# - profile: conda +# path: modules/nf-core/sentieon/dedup +# - profile: conda +# path: modules/nf-core/sentieon/qualcal +# - profile: conda +# path: modules/nf-core/spaceranger/mkgtf +# - profile: conda +# path: modules/nf-core/spaceranger/mkref +# - profile: conda +# path: modules/nf-core/spaceranger/count +# - profile: conda +# path: modules/nf-core/spotiflow +# - profile: conda +# path: modules/nf-core/svanalyzer/svbenchmark +# - profile: conda +# path: modules/nf-core/universc +# - profile: singularity +# path: modules/nf-core/universc +# - profile: conda +# path: modules/nf-core/vt/decompose +# - profile: singularity +# path: modules/nf-core/bases2fastq +# - profile: conda +# path: modules/nf-core/wittyer +# - profile: conda +# path: modules/nf-core/islandpath +# - profile: conda +# path: subworkflows/nf-core/vcf_annotate_ensemblvep +# - profile: conda +# path: subworkflows/nf-core/bcl_demultiplex +# - profile: conda +# path: subworkflows/nf-core/fastq_align_bamcmp_bwa +# - profile: conda +# path: subworkflows/nf-core/fastq_align_bwa diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml index 69d95b7d2e0..f38e2ceb35c 100644 --- a/.github/workflows/nf-test.yml +++ b/.github/workflows/nf-test.yml @@ -159,137 +159,3 @@ jobs: if: always() run: | sudo rm -rf /home/ubuntu/tests/ - -# TODO What do we do with these? -# I think we can require Docker,modules,Shard 1..Singularity,subworkflows,3 and skip the condas now -# - path: modules/nf-core/nf-test -# - profile: conda -# path: modules/nf-core/angsd/gl -# - profile: conda -# path: modules/nf-core/annotsv/installannotations -# - profile: conda -# path: modules/nf-core/happy/sompy -# - profile: conda -# path: modules/nf-core/backsub -# - profile: conda -# path: modules/nf-core/bakta/bakta -# - profile: conda -# path: modules/nf-core/bakta/baktadbdownload -# - profile: conda -# path: modules/nf-core/bases2fastq -# - profile: conda -# path: modules/nf-core/bcl2fastq -# - profile: conda -# path: modules/nf-core/bclconvert -# - profile: conda -# path: modules/nf-core/celesta -# - profile: conda -# path: modules/nf-core/cellpose -# - profile: conda -# path: modules/nf-core/cellranger/count -# - profile: conda -# path: modules/nf-core/cellranger/mkfastq -# - profile: conda -# path: modules/nf-core/cellranger/mkgtf -# - profile: conda -# path: modules/nf-core/cellranger/mkref -# - profile: conda -# path: modules/nf-core/cellranger/mkvdjref -# - profile: conda -# path: modules/nf-core/cellranger/multi -# - profile: conda -# path: modules/nf-core/cellranger/vdj -# - profile: conda -# path: modules/nf-core/checkqc -# - profile: conda -# path: modules/nf-core/custom/dumpsoftwareversions -# - profile: conda -# path: modules/nf-core/deepcell/mesmer -# - profile: conda -# path: modules/nf-core/deepvariant -# - profile: conda -# path: modules/nf-core/ensemblvep/vep -# - profile: conda -# path: modules/nf-core/fastk/fastk -# - profile: conda -# path: modules/nf-core/fastk/histex -# - profile: conda -# path: modules/nf-core/fastk/merge -# - profile: conda -# path: modules/nf-core/fcs/fcsadaptor -# - profile: conda -# path: modules/nf-core/fcs/fcsgx -# - profile: conda -# path: modules/nf-core/ganon/buildcustom -# - profile: conda -# path: modules/nf-core/ganon/classify -# - profile: conda -# path: modules/nf-core/ganon/report -# - profile: conda -# path: modules/nf-core/ganon/table -# - profile: conda -# path: modules/nf-core/gatk4/cnnscorevariants -# - profile: conda -# path: modules/nf-core/gatk4/determinegermlinecontigploidy -# - profile: conda -# path: modules/nf-core/genescopefk -# - profile: conda -# path: modules/nf-core/ilastik/multicut -# - profile: conda -# path: modules/nf-core/ilastik/pixelclassification -# - profile: conda -# path: modules/nf-core/imputeme/vcftoprs -# - profile: conda -# path: modules/nf-core/mcquant -# - profile: conda -# path: modules/nf-core/merquryfk/katcomp -# - profile: conda -# path: modules/nf-core/merquryfk/katgc -# - profile: conda -# path: modules/nf-core/merquryfk/merquryfk -# - profile: conda -# path: modules/nf-core/merquryfk/ploidyplot -# - profile: conda -# path: modules/nf-core/molkartgarage/clahe -# - profile: conda -# path: modules/nf-core/quartonotebook -# - profile: conda -# path: modules/nf-core/scimap/spatiallda -# - profile: conda -# path: modules/nf-core/sentieon/bwaindex -# - profile: conda -# path: modules/nf-core/sentieon/bwamem -# - profile: conda -# path: modules/nf-core/sentieon/dedup -# - profile: conda -# path: modules/nf-core/sentieon/qualcal -# - profile: conda -# path: modules/nf-core/spaceranger/mkgtf -# - profile: conda -# path: modules/nf-core/spaceranger/mkref -# - profile: conda -# path: modules/nf-core/spaceranger/count -# - profile: conda -# path: modules/nf-core/spotiflow -# - profile: conda -# path: modules/nf-core/svanalyzer/svbenchmark -# - profile: conda -# path: modules/nf-core/universc -# - profile: singularity -# path: modules/nf-core/universc -# - profile: conda -# path: modules/nf-core/vt/decompose -# - profile: singularity -# path: modules/nf-core/bases2fastq -# - profile: conda -# path: modules/nf-core/wittyer -# - profile: conda -# path: modules/nf-core/islandpath -# - profile: conda -# path: subworkflows/nf-core/vcf_annotate_ensemblvep -# - profile: conda -# path: subworkflows/nf-core/bcl_demultiplex -# - profile: conda -# path: subworkflows/nf-core/fastq_align_bamcmp_bwa -# - profile: conda -# path: subworkflows/nf-core/fastq_align_bwa From af2d9177793bf48c872addadf6e22dd99e0123bc Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Tue, 24 Sep 2024 07:36:57 -0500 Subject: [PATCH 21/30] ci: Address a comment --- .github/workflows/nf-test.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml index f38e2ceb35c..a6acf4f0283 100644 --- a/.github/workflows/nf-test.yml +++ b/.github/workflows/nf-test.yml @@ -52,6 +52,7 @@ jobs: steps: # TODO If conda-fail.yml exists and matrix = conda skip + # https://github.com/askimed/nf-test/issues/260 - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4 with: From 372625e1d0633338c6d2ae02dae15f754a528362 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Tue, 24 Sep 2024 08:44:10 -0500 Subject: [PATCH 22/30] style: Move prettier and editorconfig to pre-commit https://github.com/nf-core/modules/pull/4554#issuecomment-1845488824 --- .github/workflows/lint.yml | 32 -------------------------------- .pre-commit-config.yaml | 5 +++++ 2 files changed, 5 insertions(+), 32 deletions(-) diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml index bb20af0f209..42bc7b8ebcf 100644 --- a/.github/workflows/lint.yml +++ b/.github/workflows/lint.yml @@ -38,38 +38,6 @@ jobs: with: extra_args: "" - prettier: - runs-on: ubuntu-latest - steps: - - name: Check out repository - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4 - - - name: Install NodeJS - uses: actions/setup-node@1e60f620b9541d16bece96c5465dc8ee9832be0b # v4 - with: - node-version: "20" - - - name: Install Prettier - run: npm install -g prettier@3.1.0 - - - name: Run Prettier --check - run: prettier --check . - - editorconfig: - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4 - - - uses: actions/setup-node@1e60f620b9541d16bece96c5465dc8ee9832be0b # v4 - with: - node-version: "20" - - - name: Install editorconfig-checker - run: npm install -g editorconfig-checker - - - name: Run ECLint check - run: editorconfig-checker -exclude README.md $(git ls-files | grep -v test) - ################### # nf-core linting # ################### diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index d195d3d9044..056285a3ec2 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -29,3 +29,8 @@ repos: files: \.py$ args: [--fix, --exit-non-zero-on-fix, "--select", "I,E1,E4,E7,E9,F,UP,N"] # sort imports and fix (rules taken from nf-core/tools) - id: ruff-format # formatter + - repo: https://github.com/editorconfig-checker/editorconfig-checker.python + rev: "" # pick a git hash / tag to point to + hooks: + - id: editorconfig-checker + alias: ec From 1670c52b19bebed54cd9c973d30348501c7d981f Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Tue, 24 Sep 2024 08:45:34 -0500 Subject: [PATCH 23/30] ci: Add note about nf-core lint pre-commit --- .github/workflows/lint.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml index 42bc7b8ebcf..8a0b32aad6f 100644 --- a/.github/workflows/lint.yml +++ b/.github/workflows/lint.yml @@ -41,6 +41,8 @@ jobs: ################### # nf-core linting # ################### + # TODO Move these to pre-commit + # https://github.com/nf-core/tools/pull/3141 nf-core-changes: name: nf-core-changes runs-on: ubuntu-latest From adf66581a9fc63bd71b469b63f81d395dcda47e4 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Tue, 24 Sep 2024 08:53:51 -0500 Subject: [PATCH 24/30] chore: Copy over conda skips https://github.com/nf-core/modules/commit/a004c86eea62d4eed15768c0edb3adcc3f2c1424 https://github.com/nf-core/modules/commit/2da71b7a52a7c6609cb8f29d316ed3fd90d0f7cc --- .github/conda_skip.yml | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/.github/conda_skip.yml b/.github/conda_skip.yml index 44e43a740a4..801fb9616fc 100644 --- a/.github/conda_skip.yml +++ b/.github/conda_skip.yml @@ -45,6 +45,14 @@ # path: modules/nf-core/deepcell/mesmer # - profile: conda # path: modules/nf-core/deepvariant +- profile: conda + path: modules/nf-core/deepvariant/callvariants +- profile: conda + path: modules/nf-core/deepvariant/makeexamples +- profile: conda + path: modules/nf-core/deepvariant/postprocessvariants +- profile: conda + path: modules/nf-core/deepvariant/rundeepvariant # - profile: conda # path: modules/nf-core/ensemblvep/vep # - profile: conda @@ -97,6 +105,8 @@ # path: modules/nf-core/sentieon/bwaindex # - profile: conda # path: modules/nf-core/sentieon/bwamem +- profile: conda + path: modules/nf-core/sentieon/datametrics # - profile: conda # path: modules/nf-core/sentieon/dedup # - profile: conda @@ -127,6 +137,8 @@ # path: subworkflows/nf-core/vcf_annotate_ensemblvep # - profile: conda # path: subworkflows/nf-core/bcl_demultiplex +- profile: conda + path: subworkflows/nf-core/deepvariant # - profile: conda # path: subworkflows/nf-core/fastq_align_bamcmp_bwa # - profile: conda From d0caf9e6d0d4433780aa9e2c6e20a2bedf46ee1f Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Mon, 30 Sep 2024 15:17:21 -0500 Subject: [PATCH 25/30] ci: only-changed => changed-since --- .github/workflows/nf-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml index a6acf4f0283..69bab0b9ae1 100644 --- a/.github/workflows/nf-test.yml +++ b/.github/workflows/nf-test.yml @@ -143,7 +143,7 @@ jobs: --tap=test.tap \ --ci \ --verbose \ - --only-changed \ + --changed-since HEAD^ \ --shard ${{ matrix.shard }}/${{ env.TOTAL_SHARDS }} \ --filter ${{ matrix.filter }} \ --follow-dependencies From 164498a3e042d4dd048ee774b7201fb0ecf9d464 Mon Sep 17 00:00:00 2001 From: adamrtalbot <12817534+adamrtalbot@users.noreply.github.com> Date: Mon, 30 Sep 2024 19:34:53 +0100 Subject: [PATCH 26/30] Add samtools sort and unzip to stress test --- modules/nf-core/samtools/sort/tests/main.nf.test | 3 ++- modules/nf-core/unzip/tests/main.nf.test | 5 +++-- 2 files changed, 5 insertions(+), 3 deletions(-) diff --git a/modules/nf-core/samtools/sort/tests/main.nf.test b/modules/nf-core/samtools/sort/tests/main.nf.test index c2ea9c72ac1..0bc6c835842 100644 --- a/modules/nf-core/samtools/sort/tests/main.nf.test +++ b/modules/nf-core/samtools/sort/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) @@ -125,4 +126,4 @@ nextflow_process { ) } } -} +} \ No newline at end of file diff --git a/modules/nf-core/unzip/tests/main.nf.test b/modules/nf-core/unzip/tests/main.nf.test index 238b68d8ba5..df4cb5a6902 100644 --- a/modules/nf-core/unzip/tests/main.nf.test +++ b/modules/nf-core/unzip/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id: 'hello' ], file(params.modules_testdata_base_path + 'generic/tar/hello.tar.gz', checkIfExists: true) @@ -25,7 +26,7 @@ nextflow_process { assertAll( { assert process.success }, { assert snapshot(process.out).match() } - ) + ) } } @@ -51,4 +52,4 @@ nextflow_process { ) } } -} +} \ No newline at end of file From fed0e6c9827be3e89e4978e08e12dc9a74005e75 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Mon, 30 Sep 2024 15:45:53 -0500 Subject: [PATCH 27/30] dummy: Add changes to actual module files not tests --- modules/nf-core/samtools/sort/main.nf | 2 +- modules/nf-core/unzip/main.nf | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/modules/nf-core/samtools/sort/main.nf b/modules/nf-core/samtools/sort/main.nf index acfd9252ce4..246e9719502 100644 --- a/modules/nf-core/samtools/sort/main.nf +++ b/modules/nf-core/samtools/sort/main.nf @@ -29,7 +29,7 @@ process SAMTOOLS_SORT { "bam" def reference = fasta ? "--reference ${fasta}" : "" if ("$bam" == "${prefix}.bam") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" - + // Team sarek """ samtools cat \\ ${bam} \\ diff --git a/modules/nf-core/unzip/main.nf b/modules/nf-core/unzip/main.nf index a0c02109cde..0e2774959de 100644 --- a/modules/nf-core/unzip/main.nf +++ b/modules/nf-core/unzip/main.nf @@ -21,6 +21,7 @@ process UNZIP { def args = task.ext.args ?: '' if ( archive instanceof List && archive.name.size > 1 ) { error "[UNZIP] error: 7za only accepts a single archive as input. Please check module input." } prefix = task.ext.prefix ?: ( meta.id ? "${meta.id}" : archive.baseName) + // Stress test """ 7za \\ x \\ From 0b8d4e444169bca2bc157b601738021af3653cad Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Mon, 30 Sep 2024 15:59:31 -0500 Subject: [PATCH 28/30] dummy: Remove comment because malt build is borked --- modules/nf-core/unzip/main.nf | 1 - 1 file changed, 1 deletion(-) diff --git a/modules/nf-core/unzip/main.nf b/modules/nf-core/unzip/main.nf index 0e2774959de..a0c02109cde 100644 --- a/modules/nf-core/unzip/main.nf +++ b/modules/nf-core/unzip/main.nf @@ -21,7 +21,6 @@ process UNZIP { def args = task.ext.args ?: '' if ( archive instanceof List && archive.name.size > 1 ) { error "[UNZIP] error: 7za only accepts a single archive as input. Please check module input." } prefix = task.ext.prefix ?: ( meta.id ? "${meta.id}" : archive.baseName) - // Stress test """ 7za \\ x \\ From d7eb610cf3890d4f143d0b37f23c4edd6f18b1ac Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Mon, 30 Sep 2024 16:24:12 -0500 Subject: [PATCH 29/30] dummy: Touch untar --- modules/nf-core/untar/main.nf | 1 + 1 file changed, 1 insertion(+) diff --git a/modules/nf-core/untar/main.nf b/modules/nf-core/untar/main.nf index 9bd8f554611..35034eaac74 100644 --- a/modules/nf-core/untar/main.nf +++ b/modules/nf-core/untar/main.nf @@ -1,3 +1,4 @@ +// team sarek process UNTAR { tag "$archive" label 'process_single' From c9f1ed02f9603f666e5d2571b0b5bcc1d5961c0f Mon Sep 17 00:00:00 2001 From: adamrtalbot <12817534+adamrtalbot@users.noreply.github.com> Date: Tue, 1 Oct 2024 09:57:28 +0100 Subject: [PATCH 30/30] yolo --- .github/workflows/lint.yml | 150 -------- .github/workflows/pytest-workflow.yml | 343 ------------------ modules/nf-core/abacas/tests/main.nf.test | 1 + .../nf-core/abritamr/run/tests/main.nf.test | 1 + .../nf-core/adapterremoval/tests/main.nf.test | 4 + .../tests/main.nf.test | 1 + modules/nf-core/admixture/tests/main.nf.test | 2 + .../nf-core/affy/justrma/tests/main.nf.test | 3 + .../agat/convertspgff2gtf/tests/main.nf.test | 2 + .../agat/convertspgff2tsv/tests/main.nf.test | 2 + .../agat/convertspgxf2gxf/tests/main.nf.test | 2 + .../agat/spaddintrons/tests/main.nf.test | 2 + .../tests/main.nf.test | 3 + .../spmergeannotations/tests/main.nf.test | 4 + .../agat/spstatistics/tests/main.nf.test | 2 + .../agat/sqstatbasic/tests/main.nf.test | 2 + modules/nf-core/agrvate/tests/main.nf.test | 2 + modules/nf-core/ale/tests/main.nf.test | 4 + .../nf-core/allelecounter/tests/main.nf.test | 2 + modules/nf-core/ampcombi/tests/main.nf.test | 2 + .../ampcombi2/cluster/tests/main.nf.test | 2 + .../ampcombi2/complete/tests/main.nf.test | 2 + .../ampcombi2/parsetables/tests/main.nf.test | 2 + modules/nf-core/ampir/tests/main.nf.test | 2 + .../amplify/predict/tests/main.nf.test | 2 + .../amrfinderplus/run/tests/main.nf.test | 2 + .../amrfinderplus/update/tests/main.nf.test | 2 + .../angsd/contamination/tests/main.nf.test | 2 + .../nf-core/angsd/docounts/tests/main.nf.test | 1 + .../annotsv/annotsv/tests/main.nf.test | 1 + .../anota2seq/anota2seqrun/tests/main.nf.test | 1 + .../antismashlite/tests/main.nf.test | 2 + .../tests/main.nf.test | 2 + .../arcashla/extract/tests/main.nf.test | 2 + modules/nf-core/argnorm/tests/main.nf.test | 6 + modules/nf-core/aria2/tests/main.nf.test | 2 + .../nf-core/ariba/getref/tests/main.nf.test | 2 + modules/nf-core/ariba/run/tests/main.nf.test | 1 + .../arriba/download/tests/main.nf.test | 1 + .../nf-core/art/illumina/tests/main.nf.test | 4 + modules/nf-core/atlas/call/tests/main.nf.test | 1 + modules/nf-core/atlas/pmd/tests/main.nf.test | 1 + .../nf-core/atlas/recal/tests/main.nf.test | 1 + .../atlas/splitmerge/tests/main.nf.test | 1 + .../gtf2featureannotation/tests/main.nf.test | 3 + modules/nf-core/backsub/tests/main.nf.test | 1 + modules/nf-core/bacphlip/tests/main.nf.test | 1 + .../nf-core/bakta/bakta/tests/main.nf.test | 6 +- .../bakta/baktadbdownload/tests/main.nf.test | 2 + .../bam2fastx/bam2fastq/tests/main.nf.test | 1 + .../bamaligncleaner/tests/main.nf.test | 2 + modules/nf-core/bamcmp/tests/main.nf.test | 2 + .../bamstats/generalstats/tests/main.nf.test | 2 + .../nf-core/bamtofastq10x/tests/main.nf.test | 2 + .../nf-core/bamtools/stats/tests/main.nf.test | 1 + .../bamutil/trimbam/tests/main.nf.test | 1 + .../nf-core/bandage/image/tests/main.nf.test | 1 + modules/nf-core/barrnap/tests/main.nf.test | 2 + .../nf-core/bases2fastq/tests/main.nf.test | 2 + .../nf-core/bbmap/bbduk/tests/main.nf.test | 6 + .../nf-core/bbmap/bbmerge/tests/main.nf.test | 4 + .../nf-core/bbmap/bbnorm/tests/main.nf.test | 4 + .../nf-core/bbmap/bbsplit/tests/main.nf.test | 3 + .../nf-core/bbmap/clumpify/tests/main.nf.test | 2 + .../bbmap/filterbyname/tests/main.nf.test | 8 + .../nf-core/bbmap/index/tests/main.nf.test | 1 + .../nf-core/bbmap/pileup/tests/main.nf.test | 1 + .../bbmap/sendsketch/tests/main.nf.test | 2 + .../bcftools/annotate/tests/main.nf.test | 10 + .../nf-core/bcftools/call/tests/main.nf.test | 9 + .../bcftools/concat/tests/main.nf.test | 9 + .../bcftools/consensus/tests/main.nf.test | 1 + .../bcftools/filter/tests/main.nf.test | 9 + .../nf-core/bcftools/index/tests/main.nf.test | 4 + .../nf-core/bcftools/isec/tests/main.nf.test | 2 + .../nf-core/bcftools/merge/tests/main.nf.test | 21 ++ .../bcftools/mpileup/tests/main.nf.test | 6 + .../nf-core/bcftools/norm/tests/main.nf.test | 18 + .../pluginimputeinfo/tests/main.nf.test | 9 + .../bcftools/pluginscatter/tests/main.nf.test | 12 + .../bcftools/pluginsplit/tests/main.nf.test | 6 + .../bcftools/plugintag2tag/tests/main.nf.test | 9 + .../nf-core/bcftools/query/tests/main.nf.test | 3 + .../nf-core/bcftools/roh/tests/main.nf.test | 2 + .../nf-core/bcftools/sort/tests/main.nf.test | 8 + .../nf-core/bcftools/split/tests/main.nf.test | 1 + .../nf-core/bcftools/stats/tests/main.nf.test | 6 + .../nf-core/bcftools/view/tests/main.nf.test | 9 + .../nf-core/beagle5/beagle/tests/main.nf.test | 3 + .../bedops/convert2bed/tests/main.nf.test | 2 + .../nf-core/bedops/gtf2bed/tests/main.nf.test | 2 + .../bedtools/bamtobed/tests/main.nf.test | 6 +- .../bedtools/closest/tests/main.nf.test | 9 +- .../bedtools/complement/tests/main.nf.test | 3 +- .../bedtools/coverage/tests/main.nf.test | 6 +- .../bedtools/genomecov/tests/main.nf.test | 6 + .../bedtools/getfasta/tests/main.nf.test | 6 +- .../bedtools/groupby/tests/main.nf.test | 1 + .../bedtools/intersect/tests/main.nf.test | 3 + .../bedtools/jaccard/tests/main.nf.test | 2 + .../bedtools/makewindows/tests/main.nf.test | 2 + .../nf-core/bedtools/map/tests/main.nf.test | 3 + .../bedtools/maskfasta/tests/main.nf.test | 1 + .../nf-core/bedtools/merge/tests/main.nf.test | 1 + .../bedtools/multiinter/tests/main.nf.test | 2 + .../nf-core/bedtools/shift/tests/main.nf.test | 1 + 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modules/nf-core/seqkit/seq/tests/main.nf.test | 6 + .../nf-core/seqkit/sliding/tests/main.nf.test | 3 + .../nf-core/seqkit/sort/tests/main.nf.test | 6 + .../nf-core/seqkit/split2/tests/main.nf.test | 9 + .../nf-core/seqkit/stats/tests/main.nf.test | 6 + .../nf-core/seqkit/tab2fx/tests/main.nf.test | 5 + modules/nf-core/seqsero2/tests/main.nf.test | 1 + modules/nf-core/seqtk/cutn/tests/main.nf.test | 2 + .../nf-core/seqtk/mergepe/tests/main.nf.test | 3 + .../nf-core/seqtk/rename/tests/main.nf.test | 3 + .../nf-core/seqtk/sample/tests/main.nf.test | 3 + modules/nf-core/seqtk/seq/tests/main.nf.test | 3 + .../nf-core/seqtk/subseq/tests/main.nf.test | 2 + .../sequenzautils/bam2seqz/tests/main.nf.test | 2 + .../sequenzautils/gcwiggle/tests/main.nf.test | 2 + modules/nf-core/seroba/run/tests/main.nf.test | 1 + modules/nf-core/severus/tests/main.nf.test | 2 + modules/nf-core/shasta/tests/main.nf.test | 1 + modules/nf-core/shasum/tests/main.nf.test | 1 + 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modules/nf-core/star/align/tests/main.nf.test | 10 + .../star/genomegenerate/tests/main.nf.test | 4 + .../nf-core/star/starsolo/tests/main.nf.test | 2 + .../nf-core/staramr/search/tests/main.nf.test | 1 + modules/nf-core/stardist/tests/main.nf.test | 2 + modules/nf-core/stranger/tests/main.nf.test | 2 + .../strelka/germline/tests/main.nf.test | 3 + .../strelka/somatic/tests/main.nf.test | 3 + .../stringtie/merge/tests/main.nf.test | 2 + .../stringtie/stringtie/tests/main.nf.test | 8 + .../subread/featurecounts/tests/main.nf.test | 6 + .../summarizedexperiment/tests/main.nf.test | 8 + .../survivor/bedpetovcf/tests/main.nf.test | 2 + .../nf-core/survivor/merge/tests/main.nf.test | 2 + .../nf-core/survivor/stats/tests/main.nf.test | 2 + modules/nf-core/svdb/build/tests/main.nf.test | 4 + modules/nf-core/svdb/merge/tests/main.nf.test | 2 + modules/nf-core/svdb/query/tests/main.nf.test | 1 + .../svtk/countsvtypes/tests/main.nf.test | 1 + .../svtyper/svtyper/tests/main.nf.test | 2 + 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modules/nf-core/tiddit/sv/tests/main.nf.test | 5 + .../nf-core/tidk/explore/tests/main.nf.test | 3 + modules/nf-core/tidk/plot/tests/main.nf.test | 2 + .../nf-core/tidk/search/tests/main.nf.test | 4 + modules/nf-core/toulligqc/tests/main.nf.test | 5 + .../transdecoder/longorf/tests/main.nf.test | 3 + modules/nf-core/trimgalore/tests/main.nf.test | 4 + .../nf-core/trimmomatic/tests/main.nf.test | 4 + modules/nf-core/trinity/tests/main.nf.test | 5 + modules/nf-core/trust4/tests/main.nf.test | 3 + .../truvari/consistency/tests/main.nf.test | 3 + .../truvari/segment/tests/main.nf.test | 2 + .../trycycler/cluster/tests/main.nf.test | 1 + .../trycycler/subsample/tests/main.nf.test | 1 + modules/nf-core/tsebra/tests/main.nf.test | 2 + .../tximeta/tximport/tests/main.nf.test | 4 + .../nf-core/ucsc/bedclip/tests/main.nf.test | 2 + .../ucsc/bedgraphtobigwig/tests/main.nf.test | 2 + .../bigwigaverageoverbed/tests/main.nf.test | 1 + .../ucsc/gtftogenepred/tests/main.nf.test | 1 + .../nf-core/ucsc/liftover/tests/main.nf.test | 2 + .../ucsc/wigtobigwig/tests/main.nf.test | 2 + .../nf-core/umitools/dedup/tests/main.nf.test | 6 + .../umitools/extract/tests/main.nf.test | 4 + .../prepareforrsem/tests/main.nf.test | 2 + modules/nf-core/unicycler/tests/main.nf.test | 2 + modules/nf-core/untar/tests/main.nf.test | 4 + modules/nf-core/untarfiles/tests/main.nf.test | 4 + modules/nf-core/unzip/tests/main.nf.test | 1 + modules/nf-core/unzipfiles/tests/main.nf.test | 2 + modules/nf-core/upd/tests/main.nf.test | 2 + modules/nf-core/upp/align/tests/main.nf.test | 3 + modules/nf-core/variantbam/tests/main.nf.test | 2 + .../tests/main.nf.test | 2 + .../nf-core/vcf2cytosure/tests/main.nf.test | 2 + modules/nf-core/vcf2db/tests/main.nf.test | 2 + modules/nf-core/vcf2maf/tests/main.nf.test | 2 + modules/nf-core/vcfanno/tests/main.nf.test | 3 + .../vcflib/vcfbreakmulti/tests/main.nf.test | 2 + .../vcflib/vcffilter/tests/main.nf.test | 1 + .../vcflib/vcffixup/tests/main.nf.test | 2 + .../nf-core/vcflib/vcfuniq/tests/main.nf.test | 1 + modules/nf-core/vcftools/tests/main.nf.test | 5 + modules/nf-core/velocyto/tests/main.nf.test | 3 + .../verifybamid/tests/main.nf.test | 1 + .../nf-core/vg/construct/tests/main.nf.test | 4 + .../nf-core/vg/deconstruct/tests/main.nf.test | 1 + modules/nf-core/vg/index/tests/main.nf.test | 2 + .../viennarna/rnacofold/tests/main.nf.test | 2 + .../viennarna/rnafold/tests/main.nf.test | 6 +- .../viennarna/rnalfold/tests/main.nf.test | 2 + modules/nf-core/vireo/tests/main.nf.test | 2 + .../nf-core/vrhyme/vrhyme/tests/main.nf.test | 2 + .../vsearch/cluster/tests/main.nf.test | 5 + .../vsearch/dereplicate/tests/main.nf.test | 2 + .../vsearch/fastqfilter/tests/main.nf.test | 2 + .../nf-core/vsearch/sintax/tests/main.nf.test | 1 + .../nf-core/vsearch/sort/tests/main.nf.test | 2 + .../vsearch/usearchglobal/tests/main.nf.test | 2 + .../nf-core/vt/decompose/tests/main.nf.test | 2 + .../nf-core/vt/normalize/tests/main.nf.test | 4 + modules/nf-core/wfmash/tests/main.nf.test | 1 + modules/nf-core/wgsim/tests/main.nf.test | 3 + modules/nf-core/whamg/tests/main.nf.test | 1 + .../windowmasker/convert/tests/main.nf.test | 4 + .../windowmasker/mkcounts/tests/main.nf.test | 1 + .../windowmasker/ustat/tests/main.nf.test | 2 + .../wisecondorx/convert/tests/main.nf.test | 3 + .../wisecondorx/gender/tests/main.nf.test | 1 + .../wisecondorx/newref/tests/main.nf.test | 1 + .../wisecondorx/predict/tests/main.nf.test | 1 + modules/nf-core/wittyer/tests/main.nf.test | 4 + .../nf-core/xengsort/index/tests/main.nf.test | 1 + .../nf-core/xz/compress/tests/main.nf.test | 2 + .../nf-core/xz/decompress/tests/main.nf.test | 2 + modules/nf-core/yahs/tests/main.nf.test | 1 + modules/nf-core/yak/count/tests/main.nf.test | 6 +- modules/nf-core/yara/index/tests/main.nf.test | 2 + .../nf-core/yara/mapper/tests/main.nf.test | 4 + modules/nf-core/zip/tests/main.nf.test | 1 + 1015 files changed, 2671 insertions(+), 533 deletions(-) delete mode 100644 .github/workflows/lint.yml delete mode 100644 .github/workflows/pytest-workflow.yml diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml deleted file mode 100644 index 8a0b32aad6f..00000000000 --- a/.github/workflows/lint.yml +++ /dev/null @@ -1,150 +0,0 @@ -name: Run Linting -on: - pull_request: - branches: [master] - merge_group: - types: [checks_requested] - branches: [master] - workflow_dispatch: - inputs: - runners: - description: "Runners to test on" - type: choice - options: - - "ubuntu-latest" - - "self-hosted" - default: "self-hosted" - -# Cancel if a newer run is started -concurrency: - group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} - cancel-in-progress: true - -env: - NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity - NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity - GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - -jobs: - pre-commit: - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4 - - uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f # v5 - - uses: pre-commit/action@2c7b3805fd2a0fd8c1884dcaebf91fc102a13ecd # v3.0.1 - # FIXME Flip this off once we get to less than a couple hundred. Adding - # this so it will only run against changed files. It'll make it much - # easier to fix these as they come up rather than everything at once. - with: - extra_args: "" - - ################### - # nf-core linting # - ################### - # TODO Move these to pre-commit - # https://github.com/nf-core/tools/pull/3141 - nf-core-changes: - name: nf-core-changes - runs-on: ubuntu-latest - outputs: - tags: ${{ steps.filter.outputs.changes }} - modules: ${{ steps.tags.outputs.modules }} - subworkflows: ${{ steps.tags.outputs.subworkflows }} - steps: - - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4 - with: - fetch-depth: 2 # To retrieve the preceding commit. - - # TODO: change back to using dorny/paths-filter when https://github.com/dorny/paths-filter/pull/133 is implemented - - uses: mirpedrol/paths-filter@main - id: filter - with: - filters: "tests/config/pytest_modules.yml" - token: "" - - - name: Fetch module tags - id: tags - run: | - echo modules=$(echo '${{ steps.filter.outputs.changes }}' | jq -c '. | map(select(contains("modules"))) | map(gsub("modules/"; ""))') >> $GITHUB_OUTPUT - echo subworkflows=$(echo '${{ steps.filter.outputs.changes }}' | jq '. | map(select(contains("subworkflow"))) | map(gsub("subworkflows/"; ""))') >> $GITHUB_OUTPUT - - - name: debug - run: | - echo ${{ steps.tags.outputs.modules }} - echo ${{ steps.tags.outputs.subworkflows }} - - nf-core-lint-modules: - runs-on: ${{ github.event.inputs.runners || 'self-hosted' }} - name: nf-core lint modules - needs: nf-core-changes - if: ${{ (needs.nf-core-changes.outputs.modules != '[]') }} - strategy: - fail-fast: false - matrix: - tags: "${{ fromJson(needs.nf-core-changes.outputs.modules) }}" - steps: - - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4 - - - name: Set up Python - uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5 - with: - python-version: "3.11" - - - uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4 - id: cache-pip - with: - path: ~/.cache/pip - key: ${{ runner.os }}-pip - restore-keys: | - ${{ runner.os }}-pip - - - name: Install pip - run: python -m pip install --upgrade pip - - - uses: actions/setup-java@b36c23c0d998641eff861008f374ee103c25ac73 # v4 - with: - distribution: "temurin" - java-version: "17" - - - name: Setup Nextflow - uses: nf-core/setup-nextflow@v2 - - - name: Install nf-core tools development version - run: python -m pip install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git@dev - - - name: Lint module ${{ matrix.tags }} - run: nf-core modules lint ${{ matrix.tags }} - - nf-core-lint-subworkflows: - runs-on: ubuntu-latest - name: nf-core lint subworkflows - needs: nf-core-changes - if: ${{ (needs.nf-core-changes.outputs.subworkflows != '[]') }} - strategy: - fail-fast: false - matrix: - tags: "${{ fromJson(needs.nf-core-changes.outputs.subworkflows) }}" - steps: - - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4 - - - name: Set up Python - uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5 - with: - python-version: "3.11" - - - name: Install pip - run: python -m pip install --upgrade pip - - - uses: actions/setup-java@b36c23c0d998641eff861008f374ee103c25ac73 # v4 - with: - distribution: "temurin" - java-version: "17" - - - name: Setup Nextflow - uses: nf-core/setup-nextflow@561fcfc7146dcb12e3871909b635ab092a781f34 # v2 - - - name: Install nf-core tools development version - run: python -m pip install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git@dev - - - name: Lint module ${{ matrix.tags }} - run: nf-core subworkflows lint ${{ matrix.tags }} diff --git a/.github/workflows/pytest-workflow.yml b/.github/workflows/pytest-workflow.yml deleted file mode 100644 index de04a1570a8..00000000000 --- a/.github/workflows/pytest-workflow.yml +++ /dev/null @@ -1,343 +0,0 @@ -name: Run pytest-workflow -on: - pull_request: - branches: [master] - merge_group: - types: [checks_requested] - branches: [master] - workflow_dispatch: - inputs: - runners: - description: "Runners to test on" - type: choice - options: - - "ubuntu-latest" - - "self-hosted" - default: "self-hosted" - -# Cancel if a newer run is started -concurrency: - group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} - cancel-in-progress: true - -env: - NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity - NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity - GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - -jobs: - pytest-changes: - name: pytest-changes - runs-on: ubuntu-latest - outputs: - tags: ${{ steps.filter.outputs.changes }} - modules: ${{ steps.tags.outputs.modules }} - subworkflows: ${{ steps.tags.outputs.subworkflows }} - steps: - - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4 - with: - fetch-depth: 2 # To retrieve the preceding commit. - - # TODO: change back to using dorny/paths-filter when https://github.com/dorny/paths-filter/pull/133 is implemented - - uses: mirpedrol/paths-filter@main - id: filter - with: - filters: "tests/config/pytest_modules.yml" - token: "" - - - name: Fetch module tags - id: tags - run: | - echo modules=$(echo '${{ steps.filter.outputs.changes }}' | jq -c '. | map(select(contains("modules"))) | map(gsub("modules/"; ""))') >> $GITHUB_OUTPUT - echo subworkflows=$(echo '${{ steps.filter.outputs.changes }}' | jq '. | map(select(contains("subworkflow"))) | map(gsub("subworkflows/"; ""))') >> $GITHUB_OUTPUT - - - name: debug - run: | - echo ${{ steps.tags.outputs.modules }} - echo ${{ steps.tags.outputs.subworkflows }} - - pytest: - runs-on: ${{ github.event.inputs.runners || 'self-hosted' }} - name: pytest - needs: [pytest-changes] - if: needs.pytest-changes.outputs.tags != '[]' - strategy: - fail-fast: false - matrix: - tags: ["${{ fromJson(needs.pytest-changes.outputs.tags) }}"] - profile: [conda, docker, singularity] - exclude: - - tags: nf-test - - profile: conda - tags: backsub - - profile: conda - tags: bases2fastq - - profile: singularity - tags: bases2fastq - - profile: conda - tags: basicpy - - profile: conda - tags: bcl2fastq - - profile: conda - tags: bclconvert - - profile: conda - tags: bwa/aln - - profile: conda - tags: bwa/index - - profile: conda - tags: bwa/mem - - profile: conda - tags: bwa/sampe - - profile: conda - tags: bwa/samse - - profile: conda - tags: cellpose - - profile: conda - tags: cellrangerarc/count - - profile: conda - tags: cellrangerarc/mkfastq - - profile: conda - tags: cellrangerarc/mkgtf - - profile: conda - tags: cellrangerarc/mkref - - profile: conda - tags: cellrangeratac/count - - profile: conda - tags: cellrangeratac/mkfastq - - profile: conda - tags: cellrangeratac/mkref - - profile: conda - tags: checkm2/databasedownload - - profile: conda - tags: checkm2/predict - - profile: conda - tags: controlfreec/makegraph2 - - profile: conda - tags: coreograph - - profile: conda - tags: deepcell/mesmer - - profile: conda - tags: deepvariant - - profile: conda - tags: fastani - - profile: conda - tags: fastk/fastk - - profile: conda - tags: fastk/histex - - profile: conda - tags: fastk/merge - - profile: conda - tags: fcs/fcsadaptor - - profile: conda - tags: fcs/fcsgx - - profile: conda - tags: gatk4/cnnscorevariants - - profile: conda - tags: gatk4/determinegermlinecontigploidy - - profile: singularity - tags: gatk4/determinegermlinecontigploidy - - profile: conda - tags: gatk4/germlinecnvcaller - - profile: conda - tags: gatk4/postprocessgermlinecnvcalls - - profile: conda - tags: genescopefk - - profile: conda - tags: happy/sompy - - profile: conda - tags: hlala/preparegraph - - profile: conda - tags: ilastik/multicut - - profile: conda - tags: ilastik/pixelclassification - - profile: conda - tags: imputeme/vcftoprs - - profile: conda - tags: islandpath - - profile: conda - tags: manta/convertinversion - - profile: conda - tags: mcquant - - profile: conda - tags: medaka - - profile: conda - tags: merquryfk/katcomp - - profile: conda - tags: merquryfk/katgc - - profile: conda - tags: merquryfk/merquryfk - - profile: conda - tags: merquryfk/ploidyplot - - profile: conda - tags: minimap2/align - - profile: conda - tags: mitohifi/findmitoreference - - profile: conda - tags: mitohifi/mitohifi - - profile: conda - tags: nanoplot - - profile: conda - tags: ncbitools/vecscreen - - profile: conda - tags: parabricks/applybqsr - - profile: conda - tags: parabricks/dbsnp - - profile: conda - tags: parabricks/deepvariant - - profile: conda - tags: parabricks/fq2bam - - profile: conda - tags: parabricks/genotypegvcf - - profile: conda - tags: parabricks/haplotypecaller - - profile: conda - tags: parabricks/indexgvcf - - profile: conda - tags: parabricks/mutectcaller - - profile: conda - tags: picard/collecthsmetrics - - profile: conda - tags: picard/collectwgsmetrics - - profile: conda - tags: scimap/mcmicro - - profile: conda - tags: sentieon/applyvarcal - - profile: conda - tags: sentieon/datametrics - - profile: conda - tags: sentieon/dnamodelapply - - profile: conda - tags: sentieon/dnascope - - profile: conda - tags: sentieon/readwriter - - profile: conda - tags: sentieon/tnfilter - - profile: conda - tags: sentieon/tnhaplotyper2 - - profile: conda - tags: sentieon/tnscope - - profile: conda - tags: sentieon/varcal - - profile: conda - tags: sentieon/wgsmetrics - - profile: conda - tags: subworkflows/bam_qc_picard - - profile: conda - tags: subworkflows/bcl_demultiplex - - profile: conda - tags: subworkflows/fasta_clean_fcs - - profile: conda - tags: svanalyzer/svbenchmark - - profile: conda - tags: universc - - profile: singularity - tags: universc - - profile: conda - tags: vt/decompose - env: - NXF_ANSI_LOG: false - - steps: - - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4 - - - name: Set up Python - uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f # v5 - with: - python-version: "3.11" - - - uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4 - id: cache-pip-pytest - with: - path: ~/.cache/pip - key: ${{ runner.os }}-pip-pytest - restore-keys: | - ${{ runner.os }}-pip-pytest - - - name: Install Python dependencies - run: python -m pip install --upgrade pip pytest-workflow cryptography - - - uses: actions/setup-java@b36c23c0d998641eff861008f374ee103c25ac73 # v4 - with: - distribution: "temurin" - java-version: "17" - - name: Setup Nextflow ${{ matrix.NXF_VER }} - uses: nf-core/setup-nextflow@v2 - with: - version: "${{ matrix.NXF_VER }}" - - - name: Setup apptainer - if: matrix.profile == 'singularity' - uses: eWaterCycle/setup-apptainer@main - - - name: Set up Singularity - if: matrix.profile == 'singularity' - run: | - mkdir -p $NXF_SINGULARITY_CACHEDIR - mkdir -p $NXF_SINGULARITY_LIBRARYDIR - - - name: Set up miniconda - uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3 - with: - miniconda-version: "latest" - channels: conda-forge,bioconda,defaults - python-version: ${{ matrix.python-version }} - - - name: Conda setup - run: | - conda clean -a - conda install -n base conda-libmamba-solver - conda config --set solver libmamba - echo $(realpath $CONDA)/condabin >> $GITHUB_PATH - echo $(realpath python) >> $GITHUB_PATH - - # Test the module - - name: Run pytest-workflow - # only use one thread for pytest-workflow to avoid race condition on conda cache. - run: TMPDIR=~ PROFILE=${{ matrix.profile }} pytest --tag ${{ matrix.tags }} --symlink --kwdof --git-aware --color=yes - - - name: Output log on failure - if: failure() - run: | - sudo apt-get update > /dev/null - sudo apt-get install bat > /dev/null - batcat --decorations=always --color=always /home/ubuntu/pytest_workflow_*/*/log.{out,err} - - - name: Setting global variables - uses: actions/github-script@60a0d83039c74a4aee543508d2ffcb1c3799cdea # v7 - id: parsed - with: - script: | - return '${{ matrix.tags }}'.toLowerCase().replaceAll(/\//g, '-').trim('-').trim('"') - result-encoding: string - - - name: Upload logs on failure - if: failure() - uses: actions/upload-artifact@834a144ee995460fba8ed112a2fc961b36a5ec5a # v4 - with: - name: logs-${{ matrix.profile }}-${{ steps.parsed.outputs.result }} - path: | - /home/ubuntu/pytest_workflow_*/*/.nextflow.log - /home/ubuntu/pytest_workflow_*/*/log.out - /home/ubuntu/pytest_workflow_*/*/log.err - /home/ubuntu/pytest_workflow_*/*/work - !/home/ubuntu/pytest_workflow_*/*/work/conda - !/home/ubuntu/pytest_workflow_*/*/work/singularity - !${{ github.workspace }}/.singularity - - confirm-pass: - runs-on: ubuntu-latest - needs: [pytest-changes, pytest] - if: always() - steps: - - name: All tests ok - if: ${{ success() || !contains(needs.*.result, 'failure') }} - run: exit 0 - - name: One or more tests failed - if: ${{ contains(needs.*.result, 'failure') }} - run: exit 1 - - - name: debug-print - if: always() - run: | - echo "toJSON(needs) = ${{ toJSON(needs) }}" - echo "toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}" diff --git a/modules/nf-core/abacas/tests/main.nf.test b/modules/nf-core/abacas/tests/main.nf.test index daf8ac788e7..85c38417c9a 100644 --- a/modules/nf-core/abacas/tests/main.nf.test +++ b/modules/nf-core/abacas/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/scaffolds.fasta', checkIfExists: true) ] diff --git a/modules/nf-core/abritamr/run/tests/main.nf.test b/modules/nf-core/abritamr/run/tests/main.nf.test index ad0994062ac..116b465c09e 100644 --- a/modules/nf-core/abritamr/run/tests/main.nf.test +++ b/modules/nf-core/abritamr/run/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/prokaryotes/haemophilus_influenzae/genome/genome.fna.gz', checkIfExists: true) diff --git a/modules/nf-core/adapterremoval/tests/main.nf.test b/modules/nf-core/adapterremoval/tests/main.nf.test index 5b5d4227ef0..a1179ca9290 100644 --- a/modules/nf-core/adapterremoval/tests/main.nf.test +++ b/modules/nf-core/adapterremoval/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true, collapse:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) @@ -37,6 +38,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false, collapse:false ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), @@ -66,6 +68,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), @@ -94,6 +97,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false, collapse:false ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), diff --git a/modules/nf-core/adapterremovalfixprefix/tests/main.nf.test b/modules/nf-core/adapterremovalfixprefix/tests/main.nf.test index 3097c2dd4eb..6d137284738 100644 --- a/modules/nf-core/adapterremovalfixprefix/tests/main.nf.test +++ b/modules/nf-core/adapterremovalfixprefix/tests/main.nf.test @@ -55,6 +55,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = ADAPTERREMOVAL.out.collapsed """ } diff --git a/modules/nf-core/admixture/tests/main.nf.test b/modules/nf-core/admixture/tests/main.nf.test index 4bc8a62b9aa..6d07b665afe 100644 --- a/modules/nf-core/admixture/tests/main.nf.test +++ b/modules/nf-core/admixture/tests/main.nf.test @@ -28,6 +28,7 @@ nextflow_process { when { process { """ + // testy mctestface bed_ch = PLINK_VCF.out.bed bim_ch = PLINK_VCF.out.bim fam_ch = PLINK_VCF.out.fam @@ -55,6 +56,7 @@ nextflow_process { when { process { """ + // testy mctestface bed_ch = PLINK_VCF.out.bed bim_ch = PLINK_VCF.out.bim fam_ch = PLINK_VCF.out.fam diff --git a/modules/nf-core/affy/justrma/tests/main.nf.test b/modules/nf-core/affy/justrma/tests/main.nf.test index fe77d0ae0de..dbb69c3a45e 100644 --- a/modules/nf-core/affy/justrma/tests/main.nf.test +++ b/modules/nf-core/affy/justrma/tests/main.nf.test @@ -29,6 +29,7 @@ nextflow_process { when { process { """ + // testy mctestface ch_samplesheet = Channel.of([ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/array_expression/GSE38751.csv', checkIfExists: true) @@ -57,6 +58,7 @@ nextflow_process { when { process { """ + // testy mctestface ch_samplesheet = Channel.of([ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/array_expression/GSE38751.csv', checkIfExists: true) @@ -87,6 +89,7 @@ nextflow_process { when { process { """ + // testy mctestface ch_samplesheet = Channel.of([ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/array_expression/GSE38751.csv', checkIfExists: true) diff --git a/modules/nf-core/agat/convertspgff2gtf/tests/main.nf.test b/modules/nf-core/agat/convertspgff2gtf/tests/main.nf.test index 401f4552ace..20c9c616175 100644 --- a/modules/nf-core/agat/convertspgff2gtf/tests/main.nf.test +++ b/modules/nf-core/agat/convertspgff2gtf/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id: 'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gff3', checkIfExists: true) @@ -40,6 +41,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id: 'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gff3', checkIfExists: true) diff --git a/modules/nf-core/agat/convertspgff2tsv/tests/main.nf.test b/modules/nf-core/agat/convertspgff2tsv/tests/main.nf.test index 6a2e8942e26..9cfbdb0d5ef 100644 --- a/modules/nf-core/agat/convertspgff2tsv/tests/main.nf.test +++ b/modules/nf-core/agat/convertspgff2tsv/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id: 'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gff3', checkIfExists: true) @@ -38,6 +39,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id: 'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gff3', checkIfExists: true) diff --git a/modules/nf-core/agat/convertspgxf2gxf/tests/main.nf.test b/modules/nf-core/agat/convertspgxf2gxf/tests/main.nf.test index d8d7bc2d1fb..634980ab3a6 100644 --- a/modules/nf-core/agat/convertspgxf2gxf/tests/main.nf.test +++ b/modules/nf-core/agat/convertspgxf2gxf/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id: 'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gtf', checkIfExists: true) @@ -40,6 +41,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id: 'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gtf', checkIfExists: true) diff --git a/modules/nf-core/agat/spaddintrons/tests/main.nf.test b/modules/nf-core/agat/spaddintrons/tests/main.nf.test index 82d41932202..98677a8b068 100644 --- a/modules/nf-core/agat/spaddintrons/tests/main.nf.test +++ b/modules/nf-core/agat/spaddintrons/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) @@ -39,6 +40,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) diff --git a/modules/nf-core/agat/spfilterfeaturefromkilllist/tests/main.nf.test b/modules/nf-core/agat/spfilterfeaturefromkilllist/tests/main.nf.test index 82a3c307413..dcd5726f273 100644 --- a/modules/nf-core/agat/spfilterfeaturefromkilllist/tests/main.nf.test +++ b/modules/nf-core/agat/spfilterfeaturefromkilllist/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gff3', checkIfExists: true) @@ -44,6 +45,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gff3', checkIfExists: true) @@ -76,6 +78,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gff3', checkIfExists: true) diff --git a/modules/nf-core/agat/spmergeannotations/tests/main.nf.test b/modules/nf-core/agat/spmergeannotations/tests/main.nf.test index 3f500fa875f..6873c5cdb72 100644 --- a/modules/nf-core/agat/spmergeannotations/tests/main.nf.test +++ b/modules/nf-core/agat/spmergeannotations/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ @@ -45,6 +46,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ @@ -73,6 +75,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ @@ -104,6 +107,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ diff --git a/modules/nf-core/agat/spstatistics/tests/main.nf.test b/modules/nf-core/agat/spstatistics/tests/main.nf.test index ef867576850..50a89898d61 100644 --- a/modules/nf-core/agat/spstatistics/tests/main.nf.test +++ b/modules/nf-core/agat/spstatistics/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id: 'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gff3', checkIfExists: true) @@ -38,6 +39,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id: 'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gff3', checkIfExists: true) diff --git a/modules/nf-core/agat/sqstatbasic/tests/main.nf.test b/modules/nf-core/agat/sqstatbasic/tests/main.nf.test index 4803f51ed6c..f78fd0e9c85 100644 --- a/modules/nf-core/agat/sqstatbasic/tests/main.nf.test +++ b/modules/nf-core/agat/sqstatbasic/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id: 'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gff3', checkIfExists: true) @@ -38,6 +39,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id: 'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gff3', checkIfExists: true) diff --git a/modules/nf-core/agrvate/tests/main.nf.test b/modules/nf-core/agrvate/tests/main.nf.test index e196db66fc1..288cdf62a94 100644 --- a/modules/nf-core/agrvate/tests/main.nf.test +++ b/modules/nf-core/agrvate/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) @@ -41,6 +42,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) diff --git a/modules/nf-core/ale/tests/main.nf.test b/modules/nf-core/ale/tests/main.nf.test index 87c5cfa652e..d80de41128c 100644 --- a/modules/nf-core/ale/tests/main.nf.test +++ b/modules/nf-core/ale/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true), @@ -38,6 +39,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true), @@ -62,6 +64,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true), @@ -86,6 +89,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true), diff --git a/modules/nf-core/allelecounter/tests/main.nf.test b/modules/nf-core/allelecounter/tests/main.nf.test index 7a0bf13fc50..0c030626516 100644 --- a/modules/nf-core/allelecounter/tests/main.nf.test +++ b/modules/nf-core/allelecounter/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), @@ -40,6 +41,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), diff --git a/modules/nf-core/ampcombi/tests/main.nf.test b/modules/nf-core/ampcombi/tests/main.nf.test index c26421939e3..17edb7f041e 100644 --- a/modules/nf-core/ampcombi/tests/main.nf.test +++ b/modules/nf-core/ampcombi/tests/main.nf.test @@ -12,6 +12,7 @@ nextflow_process { when { process { """ + // testy mctestface amp_input = [ [id:'sample_1'], [ @@ -47,6 +48,7 @@ nextflow_process { when { process { """ + // testy mctestface amp_input = [ [id:'sample_1'], [ diff --git a/modules/nf-core/ampcombi2/cluster/tests/main.nf.test b/modules/nf-core/ampcombi2/cluster/tests/main.nf.test index 49bee6cfb10..63bc1d7fb9d 100644 --- a/modules/nf-core/ampcombi2/cluster/tests/main.nf.test +++ b/modules/nf-core/ampcombi2/cluster/tests/main.nf.test @@ -29,6 +29,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = AMPCOMBI2_COMPLETE.out.tsv """ } @@ -50,6 +51,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = AMPCOMBI2_COMPLETE.out.tsv """ } diff --git a/modules/nf-core/ampcombi2/complete/tests/main.nf.test b/modules/nf-core/ampcombi2/complete/tests/main.nf.test index 176d975faef..44dd000a59b 100644 --- a/modules/nf-core/ampcombi2/complete/tests/main.nf.test +++ b/modules/nf-core/ampcombi2/complete/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/ampcombi/ampcombi2/sample_1_ampcombi.tsv', checkIfExists: true), @@ -37,6 +38,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/ampcombi/ampcombi2/sample_1_ampcombi.tsv', checkIfExists: true), diff --git a/modules/nf-core/ampcombi2/parsetables/tests/main.nf.test b/modules/nf-core/ampcombi2/parsetables/tests/main.nf.test index 2d775179b2a..a540a87b30f 100644 --- a/modules/nf-core/ampcombi2/parsetables/tests/main.nf.test +++ b/modules/nf-core/ampcombi2/parsetables/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface amp_input = [ [id:'sample_1'], [ @@ -54,6 +55,7 @@ nextflow_process { when { process { """ + // testy mctestface amp_input = [ [id:'sample_1'], [ diff --git a/modules/nf-core/ampir/tests/main.nf.test b/modules/nf-core/ampir/tests/main.nf.test index 0ed40ef50df..2130bc79a1a 100644 --- a/modules/nf-core/ampir/tests/main.nf.test +++ b/modules/nf-core/ampir/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/proteome.fasta', checkIfExists: true), @@ -40,6 +41,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/proteome.fasta', checkIfExists: true), diff --git a/modules/nf-core/amplify/predict/tests/main.nf.test b/modules/nf-core/amplify/predict/tests/main.nf.test index 835c409c5e1..54610b3c007 100644 --- a/modules/nf-core/amplify/predict/tests/main.nf.test +++ b/modules/nf-core/amplify/predict/tests/main.nf.test @@ -40,6 +40,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = GUNZIP.out.gunzip input[1] = [] """ @@ -62,6 +63,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.fromList([ tuple([ id:'test', single_end:false ], // meta map file("test")) diff --git a/modules/nf-core/amrfinderplus/run/tests/main.nf.test b/modules/nf-core/amrfinderplus/run/tests/main.nf.test index 8103bb0fb9e..2fdf4b2f5c2 100644 --- a/modules/nf-core/amrfinderplus/run/tests/main.nf.test +++ b/modules/nf-core/amrfinderplus/run/tests/main.nf.test @@ -26,6 +26,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/prokaryotes/haemophilus_influenzae/genome/genome.fna.gz', checkIfExists: true) @@ -50,6 +51,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/prokaryotes/haemophilus_influenzae/genome/genome.fna.gz', checkIfExists: true) diff --git a/modules/nf-core/amrfinderplus/update/tests/main.nf.test b/modules/nf-core/amrfinderplus/update/tests/main.nf.test index 72ff29e6f9c..531a5cbfb4d 100644 --- a/modules/nf-core/amrfinderplus/update/tests/main.nf.test +++ b/modules/nf-core/amrfinderplus/update/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface """ } } @@ -37,6 +38,7 @@ nextflow_process { when { process { """ + // testy mctestface """ } } diff --git a/modules/nf-core/angsd/contamination/tests/main.nf.test b/modules/nf-core/angsd/contamination/tests/main.nf.test index 1b5737d012c..5460bc707f4 100644 --- a/modules/nf-core/angsd/contamination/tests/main.nf.test +++ b/modules/nf-core/angsd/contamination/tests/main.nf.test @@ -34,6 +34,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = ANGSD_DOCOUNTS.out.icounts input[1] = [ [id:'test2'], file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/angsd/HapMapChrX.gz")] @@ -60,6 +61,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = ANGSD_DOCOUNTS.out.icounts input[1] = [ [id:'test2'], file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/angsd/HapMapChrX.gz")] diff --git a/modules/nf-core/angsd/docounts/tests/main.nf.test b/modules/nf-core/angsd/docounts/tests/main.nf.test index 68993421b82..e3cea9598ba 100644 --- a/modules/nf-core/angsd/docounts/tests/main.nf.test +++ b/modules/nf-core/angsd/docounts/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam', checkIfExists: true), diff --git a/modules/nf-core/annotsv/annotsv/tests/main.nf.test b/modules/nf-core/annotsv/annotsv/tests/main.nf.test index c6fcefb66e3..686a7ca1ef7 100644 --- a/modules/nf-core/annotsv/annotsv/tests/main.nf.test +++ b/modules/nf-core/annotsv/annotsv/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/vcf/sv_query.vcf.gz"), diff --git a/modules/nf-core/anota2seq/anota2seqrun/tests/main.nf.test b/modules/nf-core/anota2seq/anota2seqrun/tests/main.nf.test index ed9aa46336a..a98adc4339d 100644 --- a/modules/nf-core/anota2seq/anota2seqrun/tests/main.nf.test +++ b/modules/nf-core/anota2seq/anota2seqrun/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'treatment_vs_control'], // meta map 'treatment', diff --git a/modules/nf-core/antismash/antismashlite/tests/main.nf.test b/modules/nf-core/antismash/antismashlite/tests/main.nf.test index 5ee21d6ded4..e13ade2c56b 100644 --- a/modules/nf-core/antismash/antismashlite/tests/main.nf.test +++ b/modules/nf-core/antismash/antismashlite/tests/main.nf.test @@ -78,6 +78,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = GUNZIP.out.gunzip input[1] = ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES.out.database input[2] = ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES.out.antismash_dir @@ -108,6 +109,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = GUNZIP.out.gunzip input[1] = ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES.out.database input[2] = ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES.out.antismash_dir diff --git a/modules/nf-core/antismash/antismashlitedownloaddatabases/tests/main.nf.test b/modules/nf-core/antismash/antismashlitedownloaddatabases/tests/main.nf.test index 55f5f2f50a1..5f83a2c562a 100644 --- a/modules/nf-core/antismash/antismashlitedownloaddatabases/tests/main.nf.test +++ b/modules/nf-core/antismash/antismashlitedownloaddatabases/tests/main.nf.test @@ -54,6 +54,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = UNTAR_CSS.out.untar.map{ it[1] } input[1] = UNTAR_DETECTION.out.untar.map{ it[1] } input[2] = UNTAR_MODULES.out.untar.map{ it[1] } @@ -118,6 +119,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = UNTAR_CSS.out.untar.map{ it[1] } input[1] = UNTAR_DETECTION.out.untar.map{ it[1] } input[2] = UNTAR_MODULES.out.untar.map{ it[1] } diff --git a/modules/nf-core/arcashla/extract/tests/main.nf.test b/modules/nf-core/arcashla/extract/tests/main.nf.test index 273bece876f..68a7724ea0b 100644 --- a/modules/nf-core/arcashla/extract/tests/main.nf.test +++ b/modules/nf-core/arcashla/extract/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) @@ -45,6 +46,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test_single_end', single_end:true ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test3.single_end.markduplicates.sorted.bam', checkIfExists: true) diff --git a/modules/nf-core/argnorm/tests/main.nf.test b/modules/nf-core/argnorm/tests/main.nf.test index e68c2151865..54251c7093b 100644 --- a/modules/nf-core/argnorm/tests/main.nf.test +++ b/modules/nf-core/argnorm/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'argnorm_raw.tsv' ], // meta map file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/amrfinderplus/test_output.tsv", checkIfExists: true) @@ -37,6 +38,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'argnorm_hamronized.tsv' ], // meta map file("https://raw.githubusercontent.com/BigDataBiology/argNorm/main/examples/hamronized/amrfinderplus.ncbi.orfs.tsv", checkIfExists: true) @@ -60,6 +62,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'argnorm_raw.tsv' ], // meta map file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/amrfinderplus/test_output.tsv", checkIfExists: true) @@ -83,6 +86,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'argnorm_raw.tsv' ], // meta map file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/amrfinderplus/test_output.tsv", checkIfExists: true) @@ -108,6 +112,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'argnorm_hamronized_stub.tsv' ], // meta map file("https://raw.githubusercontent.com/BigDataBiology/argNorm/main/examples/hamronized/amrfinderplus.ncbi.orfs.tsv", checkIfExists: true) @@ -134,6 +139,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'argnorm_raw_stub.tsv' ], // meta map file("https://raw.githubusercontent.com/BigDataBiology/argNorm/main/examples/raw/amrfinderplus.ncbi.orfs.tsv", checkIfExists: true) diff --git a/modules/nf-core/aria2/tests/main.nf.test b/modules/nf-core/aria2/tests/main.nf.test index ba033513e13..bd704704709 100644 --- a/modules/nf-core/aria2/tests/main.nf.test +++ b/modules/nf-core/aria2/tests/main.nf.test @@ -10,6 +10,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map params.test_data['sarscov2']['illumina']['test_single_end_bam'] // https URL ] @@ -29,6 +30,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map params.test_data['sarscov2']['illumina']['test_single_end_bam'] // https URL ] diff --git a/modules/nf-core/ariba/getref/tests/main.nf.test b/modules/nf-core/ariba/getref/tests/main.nf.test index a69065e5c6a..dec5f5659ef 100644 --- a/modules/nf-core/ariba/getref/tests/main.nf.test +++ b/modules/nf-core/ariba/getref/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map "card" ] @@ -37,6 +38,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map "card" ] diff --git a/modules/nf-core/ariba/run/tests/main.nf.test b/modules/nf-core/ariba/run/tests/main.nf.test index f51abc29e0d..6de33a67fc3 100644 --- a/modules/nf-core/ariba/run/tests/main.nf.test +++ b/modules/nf-core/ariba/run/tests/main.nf.test @@ -28,6 +28,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), diff --git a/modules/nf-core/arriba/download/tests/main.nf.test b/modules/nf-core/arriba/download/tests/main.nf.test index cccc95db2c0..4110951829b 100644 --- a/modules/nf-core/arriba/download/tests/main.nf.test +++ b/modules/nf-core/arriba/download/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface """ } diff --git a/modules/nf-core/art/illumina/tests/main.nf.test b/modules/nf-core/art/illumina/tests/main.nf.test index f40fa18bbdc..51ff19240f3 100644 --- a/modules/nf-core/art/illumina/tests/main.nf.test +++ b/modules/nf-core/art/illumina/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id: 'test'], [ @@ -59,6 +60,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id: 'test'], [ @@ -88,6 +90,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id: 'test'], [ @@ -144,6 +147,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id: 'test'], [ diff --git a/modules/nf-core/atlas/call/tests/main.nf.test b/modules/nf-core/atlas/call/tests/main.nf.test index dbd40640873..81fb34d33d8 100644 --- a/modules/nf-core/atlas/call/tests/main.nf.test +++ b/modules/nf-core/atlas/call/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), diff --git a/modules/nf-core/atlas/pmd/tests/main.nf.test b/modules/nf-core/atlas/pmd/tests/main.nf.test index fc804e7b170..5eb30c723c0 100644 --- a/modules/nf-core/atlas/pmd/tests/main.nf.test +++ b/modules/nf-core/atlas/pmd/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), diff --git a/modules/nf-core/atlas/recal/tests/main.nf.test b/modules/nf-core/atlas/recal/tests/main.nf.test index e03c6208b36..df4b83ad1c5 100644 --- a/modules/nf-core/atlas/recal/tests/main.nf.test +++ b/modules/nf-core/atlas/recal/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), diff --git a/modules/nf-core/atlas/splitmerge/tests/main.nf.test b/modules/nf-core/atlas/splitmerge/tests/main.nf.test index 9d7d1884b97..8d1ee8d1898 100644 --- a/modules/nf-core/atlas/splitmerge/tests/main.nf.test +++ b/modules/nf-core/atlas/splitmerge/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), diff --git a/modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/tests/main.nf.test b/modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/tests/main.nf.test index 74c0c318680..9c17350a103 100644 --- a/modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/tests/main.nf.test +++ b/modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ "id":"homo_sapiens" ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.gtf") @@ -38,6 +39,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ "id":"homo_sapiens" ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.gtf") @@ -66,6 +68,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ "id":"homo_sapiens" ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.gtf") diff --git a/modules/nf-core/backsub/tests/main.nf.test b/modules/nf-core/backsub/tests/main.nf.test index 7b79d9f576d..cdebfb3f6c5 100644 --- a/modules/nf-core/backsub/tests/main.nf.test +++ b/modules/nf-core/backsub/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface // define inputs of the process here. Example: input[0] = [ [ id:'test' ], diff --git a/modules/nf-core/bacphlip/tests/main.nf.test b/modules/nf-core/bacphlip/tests/main.nf.test index 4c3f1b8b7b5..d0a342ee84f 100644 --- a/modules/nf-core/bacphlip/tests/main.nf.test +++ b/modules/nf-core/bacphlip/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/genome.fasta', checkIfExists: true) // genome.fasta diff --git a/modules/nf-core/bakta/bakta/tests/main.nf.test b/modules/nf-core/bakta/bakta/tests/main.nf.test index 3c1f8f82824..e4bc1a082ee 100644 --- a/modules/nf-core/bakta/bakta/tests/main.nf.test +++ b/modules/nf-core/bakta/bakta/tests/main.nf.test @@ -25,7 +25,8 @@ nextflow_process { when { process { - """ + """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/fasta/test1.contigs.fa.gz', checkIfExists: true) @@ -62,7 +63,8 @@ nextflow_process { when { process { - """ + """ + // testy mctestface input[0] = [[id: 'stub'],file('stub')] input[1] = [] input[2] = [] diff --git a/modules/nf-core/bakta/baktadbdownload/tests/main.nf.test b/modules/nf-core/bakta/baktadbdownload/tests/main.nf.test index a5f827f9850..763474a56ea 100644 --- a/modules/nf-core/bakta/baktadbdownload/tests/main.nf.test +++ b/modules/nf-core/bakta/baktadbdownload/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface """ } } @@ -36,6 +37,7 @@ nextflow_process { when { process { """ + // testy mctestface """ } } diff --git a/modules/nf-core/bam2fastx/bam2fastq/tests/main.nf.test b/modules/nf-core/bam2fastx/bam2fastq/tests/main.nf.test index 0d4f80ae699..6982521fe5a 100644 --- a/modules/nf-core/bam2fastx/bam2fastq/tests/main.nf.test +++ b/modules/nf-core/bam2fastx/bam2fastq/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/alz.bam', checkIfExists: true), diff --git a/modules/nf-core/bamaligncleaner/tests/main.nf.test b/modules/nf-core/bamaligncleaner/tests/main.nf.test index 3dfd7c51008..b46439102d6 100644 --- a/modules/nf-core/bamaligncleaner/tests/main.nf.test +++ b/modules/nf-core/bamaligncleaner/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.single_end.sorted.bam", checkIfExists: true) @@ -45,6 +46,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.single_end.sorted.bam", checkIfExists: true) diff --git a/modules/nf-core/bamcmp/tests/main.nf.test b/modules/nf-core/bamcmp/tests/main.nf.test index cc230858aea..278ecb73e05 100644 --- a/modules/nf-core/bamcmp/tests/main.nf.test +++ b/modules/nf-core/bamcmp/tests/main.nf.test @@ -67,6 +67,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = BWA_MEM_HUMAN.out.bam.join(BWA_MEM_COV2.out.bam) """ } @@ -88,6 +89,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id: 'test'], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) ] diff --git a/modules/nf-core/bamstats/generalstats/tests/main.nf.test b/modules/nf-core/bamstats/generalstats/tests/main.nf.test index d243f1a77ee..a4f262b85e9 100644 --- a/modules/nf-core/bamstats/generalstats/tests/main.nf.test +++ b/modules/nf-core/bamstats/generalstats/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.bam', checkIfExists: true) @@ -39,6 +40,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.bam', checkIfExists: true) diff --git a/modules/nf-core/bamtofastq10x/tests/main.nf.test b/modules/nf-core/bamtofastq10x/tests/main.nf.test index 2b455ae8447..d42822bb8c9 100644 --- a/modules/nf-core/bamtofastq10x/tests/main.nf.test +++ b/modules/nf-core/bamtofastq10x/tests/main.nf.test @@ -12,6 +12,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/10xgenomics/10x_cr12.bam', checkIfExists: true) @@ -37,6 +38,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/10xgenomics/10x_cr12.bam', checkIfExists: true) diff --git a/modules/nf-core/bamtools/stats/tests/main.nf.test b/modules/nf-core/bamtools/stats/tests/main.nf.test index 478a6f0e84d..6a8f19d395d 100644 --- a/modules/nf-core/bamtools/stats/tests/main.nf.test +++ b/modules/nf-core/bamtools/stats/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) diff --git a/modules/nf-core/bamutil/trimbam/tests/main.nf.test b/modules/nf-core/bamutil/trimbam/tests/main.nf.test index 6ce0bbdd2aa..ef8e26c9a91 100644 --- a/modules/nf-core/bamutil/trimbam/tests/main.nf.test +++ b/modules/nf-core/bamutil/trimbam/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true), diff --git a/modules/nf-core/bandage/image/tests/main.nf.test b/modules/nf-core/bandage/image/tests/main.nf.test index 160281f9b83..fe8c8754862 100644 --- a/modules/nf-core/bandage/image/tests/main.nf.test +++ b/modules/nf-core/bandage/image/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'B-3106' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/gfa/assembly.gfa', checkIfExists: true) diff --git a/modules/nf-core/barrnap/tests/main.nf.test b/modules/nf-core/barrnap/tests/main.nf.test index b2d62163209..29a22bf025a 100644 --- a/modules/nf-core/barrnap/tests/main.nf.test +++ b/modules/nf-core/barrnap/tests/main.nf.test @@ -12,6 +12,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/contigs.fasta', checkIfExists: true), @@ -36,6 +37,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/contigs.fasta', checkIfExists: true), diff --git a/modules/nf-core/bases2fastq/tests/main.nf.test b/modules/nf-core/bases2fastq/tests/main.nf.test index 4c7139c0908..8c1f5003cbd 100644 --- a/modules/nf-core/bases2fastq/tests/main.nf.test +++ b/modules/nf-core/bases2fastq/tests/main.nf.test @@ -24,6 +24,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0]= UNTAR.out.untar.map{meta, untar -> [meta, meta.samplesheet, untar]} """ @@ -54,6 +55,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0]= UNTAR.out.untar.map{meta, untar -> [meta, meta.samplesheet, untar]} """ diff --git a/modules/nf-core/bbmap/bbduk/tests/main.nf.test b/modules/nf-core/bbmap/bbduk/tests/main.nf.test index 0f3e8187052..96da0adaa24 100644 --- a/modules/nf-core/bbmap/bbduk/tests/main.nf.test +++ b/modules/nf-core/bbmap/bbduk/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ] @@ -40,6 +41,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), @@ -66,6 +68,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ] @@ -93,6 +96,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), @@ -123,6 +127,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ] @@ -148,6 +153,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), diff --git a/modules/nf-core/bbmap/bbmerge/tests/main.nf.test b/modules/nf-core/bbmap/bbmerge/tests/main.nf.test index 405f4f6360c..9290785b91f 100644 --- a/modules/nf-core/bbmap/bbmerge/tests/main.nf.test +++ b/modules/nf-core/bbmap/bbmerge/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map @@ -41,6 +42,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map @@ -67,6 +69,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map @@ -94,6 +97,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map diff --git a/modules/nf-core/bbmap/bbnorm/tests/main.nf.test b/modules/nf-core/bbmap/bbnorm/tests/main.nf.test index fc17dc1c8fa..6b8d6c5207b 100644 --- a/modules/nf-core/bbmap/bbnorm/tests/main.nf.test +++ b/modules/nf-core/bbmap/bbnorm/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) @@ -43,6 +44,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ @@ -73,6 +75,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz', checkIfExists: true) ] @@ -100,6 +103,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id:'test', single_end:true ], [ diff --git a/modules/nf-core/bbmap/bbsplit/tests/main.nf.test b/modules/nf-core/bbmap/bbsplit/tests/main.nf.test index 1f260d5f6de..9d501dcccc8 100644 --- a/modules/nf-core/bbmap/bbsplit/tests/main.nf.test +++ b/modules/nf-core/bbmap/bbsplit/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [[:], []] input[1] = [] input[2] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)) @@ -42,6 +43,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [[:], []] input[1] = [] input[2] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)) @@ -168,6 +170,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:true ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) diff --git a/modules/nf-core/bbmap/clumpify/tests/main.nf.test b/modules/nf-core/bbmap/clumpify/tests/main.nf.test index f43b8767964..203e51b8650 100644 --- a/modules/nf-core/bbmap/clumpify/tests/main.nf.test +++ b/modules/nf-core/bbmap/clumpify/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map [ @@ -44,6 +45,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ diff --git a/modules/nf-core/bbmap/filterbyname/tests/main.nf.test b/modules/nf-core/bbmap/filterbyname/tests/main.nf.test index 17c7ea5f825..7201d16b919 100644 --- a/modules/nf-core/bbmap/filterbyname/tests/main.nf.test +++ b/modules/nf-core/bbmap/filterbyname/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), @@ -42,6 +43,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), @@ -68,6 +70,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) @@ -93,6 +96,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) @@ -118,6 +122,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) @@ -143,6 +148,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) @@ -168,6 +174,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), @@ -194,6 +201,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), diff --git a/modules/nf-core/bbmap/index/tests/main.nf.test b/modules/nf-core/bbmap/index/tests/main.nf.test index 7fe4cedeff1..6307341b928 100644 --- a/modules/nf-core/bbmap/index/tests/main.nf.test +++ b/modules/nf-core/bbmap/index/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) """ diff --git a/modules/nf-core/bbmap/pileup/tests/main.nf.test b/modules/nf-core/bbmap/pileup/tests/main.nf.test index 583f407f770..ba502da8c9a 100644 --- a/modules/nf-core/bbmap/pileup/tests/main.nf.test +++ b/modules/nf-core/bbmap/pileup/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) diff --git a/modules/nf-core/bbmap/sendsketch/tests/main.nf.test b/modules/nf-core/bbmap/sendsketch/tests/main.nf.test index 744feadfcb1..edd7c416a10 100644 --- a/modules/nf-core/bbmap/sendsketch/tests/main.nf.test +++ b/modules/nf-core/bbmap/sendsketch/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true], // meta map [ @@ -43,6 +44,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false], // meta map [ diff --git a/modules/nf-core/bcftools/annotate/tests/main.nf.test b/modules/nf-core/bcftools/annotate/tests/main.nf.test index 3a5c493314f..a833d0a5f2d 100644 --- a/modules/nf-core/bcftools/annotate/tests/main.nf.test +++ b/modules/nf-core/bcftools/annotate/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), @@ -47,6 +48,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), @@ -77,6 +79,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), @@ -111,6 +114,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), @@ -145,6 +149,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), @@ -178,6 +183,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), @@ -213,6 +219,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), @@ -242,6 +249,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), @@ -272,6 +280,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), @@ -302,6 +311,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), diff --git a/modules/nf-core/bcftools/call/tests/main.nf.test b/modules/nf-core/bcftools/call/tests/main.nf.test index 31c86efc046..b7291b2d242 100644 --- a/modules/nf-core/bcftools/call/tests/main.nf.test +++ b/modules/nf-core/bcftools/call/tests/main.nf.test @@ -17,6 +17,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'out', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), @@ -48,6 +49,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'out', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), @@ -82,6 +84,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'out', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), @@ -116,6 +119,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'out', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), @@ -150,6 +154,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'out', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), @@ -182,6 +187,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'out', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), @@ -214,6 +220,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'out', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), @@ -244,6 +251,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'out', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), @@ -274,6 +282,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'out', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), diff --git a/modules/nf-core/bcftools/concat/tests/main.nf.test b/modules/nf-core/bcftools/concat/tests/main.nf.test index cb4642b29cd..60b35ad15dc 100644 --- a/modules/nf-core/bcftools/concat/tests/main.nf.test +++ b/modules/nf-core/bcftools/concat/tests/main.nf.test @@ -17,6 +17,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test3' ], // meta map [ @@ -48,6 +49,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test3' ], // meta map [ @@ -85,6 +87,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test3' ], // meta map [ @@ -122,6 +125,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test3' ], // meta map [ @@ -160,6 +164,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test3' ], // meta map [ @@ -189,6 +194,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test3' ], // meta map [ @@ -221,6 +227,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test3' ], // meta map [ @@ -254,6 +261,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test3' ], // meta map [ @@ -287,6 +295,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test3' ], // meta map [ diff --git a/modules/nf-core/bcftools/consensus/tests/main.nf.test b/modules/nf-core/bcftools/consensus/tests/main.nf.test index 567c78bc65c..aff86ca2de4 100644 --- a/modules/nf-core/bcftools/consensus/tests/main.nf.test +++ b/modules/nf-core/bcftools/consensus/tests/main.nf.test @@ -69,6 +69,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true), diff --git a/modules/nf-core/bcftools/filter/tests/main.nf.test b/modules/nf-core/bcftools/filter/tests/main.nf.test index 646f37adaec..383fd2de076 100644 --- a/modules/nf-core/bcftools/filter/tests/main.nf.test +++ b/modules/nf-core/bcftools/filter/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id:"vcf_test"], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) @@ -40,6 +41,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id:"vcf_test"], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) @@ -70,6 +72,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id:"vcf_test"], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) @@ -100,6 +103,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id:"vcf_test"], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) @@ -130,6 +134,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id:"bcf_test"], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) @@ -155,6 +160,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id:"vcf_test"], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) @@ -180,6 +186,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id:"vcf_test"], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) @@ -206,6 +213,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id:"vcf_test"], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) @@ -232,6 +240,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id:"vcf_test"], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) diff --git a/modules/nf-core/bcftools/index/tests/main.nf.test b/modules/nf-core/bcftools/index/tests/main.nf.test index 9b3748533cd..0e7bbf818bf 100644 --- a/modules/nf-core/bcftools/index/tests/main.nf.test +++ b/modules/nf-core/bcftools/index/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true) @@ -41,6 +42,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true) @@ -68,6 +70,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true) @@ -93,6 +96,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true) diff --git a/modules/nf-core/bcftools/isec/tests/main.nf.test b/modules/nf-core/bcftools/isec/tests/main.nf.test index ca8fc6e32eb..c3174e374ce 100644 --- a/modules/nf-core/bcftools/isec/tests/main.nf.test +++ b/modules/nf-core/bcftools/isec/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ @@ -55,6 +56,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ diff --git a/modules/nf-core/bcftools/merge/tests/main.nf.test b/modules/nf-core/bcftools/merge/tests/main.nf.test index 3995fc1a91b..5588bad16ad 100644 --- a/modules/nf-core/bcftools/merge/tests/main.nf.test +++ b/modules/nf-core/bcftools/merge/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ @@ -54,6 +55,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ @@ -92,6 +94,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ @@ -130,6 +133,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ @@ -168,6 +172,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ @@ -206,6 +211,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ @@ -287,6 +293,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ @@ -327,6 +334,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ @@ -368,6 +376,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ @@ -414,6 +423,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ @@ -451,6 +461,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ @@ -487,6 +498,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ @@ -523,6 +535,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ @@ -559,6 +572,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ @@ -595,6 +609,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ @@ -631,6 +646,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ @@ -668,6 +684,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ @@ -705,6 +722,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ @@ -742,6 +760,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ @@ -780,6 +799,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ @@ -825,6 +845,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ diff --git a/modules/nf-core/bcftools/mpileup/tests/main.nf.test b/modules/nf-core/bcftools/mpileup/tests/main.nf.test index 665a349fc8a..903d516f8e6 100644 --- a/modules/nf-core/bcftools/mpileup/tests/main.nf.test +++ b/modules/nf-core/bcftools/mpileup/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), @@ -49,6 +50,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), @@ -80,6 +82,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), @@ -114,6 +117,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), @@ -146,6 +150,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), @@ -179,6 +184,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), diff --git a/modules/nf-core/bcftools/norm/tests/main.nf.test b/modules/nf-core/bcftools/norm/tests/main.nf.test index dbc41502376..c9d85552017 100644 --- a/modules/nf-core/bcftools/norm/tests/main.nf.test +++ b/modules/nf-core/bcftools/norm/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), @@ -45,6 +46,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), @@ -78,6 +80,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), @@ -111,6 +114,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), @@ -144,6 +148,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), @@ -173,6 +178,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), @@ -202,6 +208,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), @@ -236,6 +243,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), @@ -265,6 +273,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), @@ -295,6 +304,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), @@ -325,6 +335,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), @@ -355,6 +366,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), @@ -384,6 +396,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), @@ -414,6 +427,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), @@ -444,6 +458,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), @@ -474,6 +489,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), @@ -505,6 +521,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), @@ -536,6 +553,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), diff --git a/modules/nf-core/bcftools/pluginimputeinfo/tests/main.nf.test b/modules/nf-core/bcftools/pluginimputeinfo/tests/main.nf.test index b150b12c7cb..9817b70831b 100644 --- a/modules/nf-core/bcftools/pluginimputeinfo/tests/main.nf.test +++ b/modules/nf-core/bcftools/pluginimputeinfo/tests/main.nf.test @@ -34,6 +34,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = BCFTOOLS_PLUGINTAG2TAG.out.vcf.join(BCFTOOLS_PLUGINTAG2TAG.out.tbi) input[1] = [] input[2] = [] @@ -77,6 +78,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = BCFTOOLS_PLUGINTAG2TAG.out.vcf.join(BCFTOOLS_PLUGINTAG2TAG.out.tbi) input[1] = [] input[2] = [] @@ -123,6 +125,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = BCFTOOLS_PLUGINTAG2TAG.out.vcf.join(BCFTOOLS_PLUGINTAG2TAG.out.tbi) input[1] = [] input[2] = [] @@ -169,6 +172,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = BCFTOOLS_PLUGINTAG2TAG.out.vcf.join(BCFTOOLS_PLUGINTAG2TAG.out.tbi) input[1] = [] input[2] = [] @@ -215,6 +219,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = BCFTOOLS_PLUGINTAG2TAG.out.vcf.join(BCFTOOLS_PLUGINTAG2TAG.out.tbi) input[1] = [] input[2] = [] @@ -259,6 +264,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = BCFTOOLS_PLUGINTAG2TAG.out.vcf.join(BCFTOOLS_PLUGINTAG2TAG.out.tbi) input[1] = [] input[2] = [] @@ -303,6 +309,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = BCFTOOLS_PLUGINTAG2TAG.out.vcf.join(BCFTOOLS_PLUGINTAG2TAG.out.tbi) input[1] = [] input[2] = [] @@ -345,6 +352,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = BCFTOOLS_PLUGINTAG2TAG.out.vcf.join(BCFTOOLS_PLUGINTAG2TAG.out.tbi) input[1] = [] input[2] = [] @@ -387,6 +395,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = BCFTOOLS_PLUGINTAG2TAG.out.vcf.join(BCFTOOLS_PLUGINTAG2TAG.out.tbi) input[1] = [] input[2] = [] diff --git a/modules/nf-core/bcftools/pluginscatter/tests/main.nf.test b/modules/nf-core/bcftools/pluginscatter/tests/main.nf.test index ce66336e0e9..d431a7673ec 100644 --- a/modules/nf-core/bcftools/pluginscatter/tests/main.nf.test +++ b/modules/nf-core/bcftools/pluginscatter/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz', checkIfExists: true), @@ -47,6 +48,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz', checkIfExists: true), @@ -83,6 +85,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz', checkIfExists: true), @@ -119,6 +122,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz', checkIfExists: true), @@ -155,6 +159,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz', checkIfExists: true), @@ -188,6 +193,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz', checkIfExists: true), @@ -223,6 +229,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz', checkIfExists: true), @@ -255,6 +262,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz', checkIfExists: true), @@ -289,6 +297,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz', checkIfExists: true), @@ -324,6 +333,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz', checkIfExists: true), @@ -356,6 +366,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz', checkIfExists: true), @@ -388,6 +399,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz', checkIfExists: true), diff --git a/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test b/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test index e3160851893..268f8e244f0 100644 --- a/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test +++ b/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz', checkIfExists: true), @@ -42,6 +43,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz', checkIfExists: true), @@ -73,6 +75,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz', checkIfExists: true), @@ -106,6 +109,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz', checkIfExists: true), @@ -136,6 +140,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz', checkIfExists: true), @@ -167,6 +172,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz', checkIfExists: true), diff --git a/modules/nf-core/bcftools/plugintag2tag/tests/main.nf.test b/modules/nf-core/bcftools/plugintag2tag/tests/main.nf.test index b9fdc6252c7..6894946e2fa 100644 --- a/modules/nf-core/bcftools/plugintag2tag/tests/main.nf.test +++ b/modules/nf-core/bcftools/plugintag2tag/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'out', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), @@ -47,6 +48,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'out', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), @@ -80,6 +82,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'out', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), @@ -113,6 +116,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'out', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), @@ -146,6 +150,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'out', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), @@ -177,6 +182,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'out', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), @@ -208,6 +214,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'out', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), @@ -237,6 +244,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'out', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), @@ -266,6 +274,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'out', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), diff --git a/modules/nf-core/bcftools/query/tests/main.nf.test b/modules/nf-core/bcftools/query/tests/main.nf.test index 39e67b35ad3..6fd830b13da 100644 --- a/modules/nf-core/bcftools/query/tests/main.nf.test +++ b/modules/nf-core/bcftools/query/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'out' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), @@ -45,6 +46,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'out' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), @@ -74,6 +76,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'out' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), diff --git a/modules/nf-core/bcftools/roh/tests/main.nf.test b/modules/nf-core/bcftools/roh/tests/main.nf.test index bb73b80c024..c563fca25c5 100644 --- a/modules/nf-core/bcftools/roh/tests/main.nf.test +++ b/modules/nf-core/bcftools/roh/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true) @@ -42,6 +43,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true) diff --git a/modules/nf-core/bcftools/sort/tests/main.nf.test b/modules/nf-core/bcftools/sort/tests/main.nf.test index b9bdd76a09f..48165dffa91 100644 --- a/modules/nf-core/bcftools/sort/tests/main.nf.test +++ b/modules/nf-core/bcftools/sort/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) @@ -37,6 +38,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) @@ -67,6 +69,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) @@ -97,6 +100,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) @@ -125,6 +129,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) @@ -150,6 +155,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) @@ -176,6 +182,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) @@ -202,6 +209,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) diff --git a/modules/nf-core/bcftools/split/tests/main.nf.test b/modules/nf-core/bcftools/split/tests/main.nf.test index 00328b2004c..cd96125cafd 100644 --- a/modules/nf-core/bcftools/split/tests/main.nf.test +++ b/modules/nf-core/bcftools/split/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true), diff --git a/modules/nf-core/bcftools/stats/tests/main.nf.test b/modules/nf-core/bcftools/stats/tests/main.nf.test index be618b0b17a..be674933ef7 100644 --- a/modules/nf-core/bcftools/stats/tests/main.nf.test +++ b/modules/nf-core/bcftools/stats/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), []] @@ -41,6 +42,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'regions_test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)] @@ -69,6 +71,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'targets_test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), [] ] @@ -98,6 +101,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'exon_test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), [] ] @@ -126,6 +130,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'ref_test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), [] ] @@ -158,6 +163,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), []] diff --git a/modules/nf-core/bcftools/view/tests/main.nf.test b/modules/nf-core/bcftools/view/tests/main.nf.test index 1e60c50d5a3..26d1bb83e7c 100644 --- a/modules/nf-core/bcftools/view/tests/main.nf.test +++ b/modules/nf-core/bcftools/view/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'out', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), @@ -47,6 +48,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'out', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), @@ -81,6 +83,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'out', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), @@ -115,6 +118,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'out', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), @@ -149,6 +153,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'out', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), @@ -181,6 +186,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'out', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), @@ -213,6 +219,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'out', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), @@ -243,6 +250,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'out', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), @@ -273,6 +281,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'out', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), diff --git a/modules/nf-core/beagle5/beagle/tests/main.nf.test b/modules/nf-core/beagle5/beagle/tests/main.nf.test index 2763708e273..02dd4783eab 100644 --- a/modules/nf-core/beagle5/beagle/tests/main.nf.test +++ b/modules/nf-core/beagle5/beagle/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/beagle/target.22Jul22.46e.vcf.gz", checkIfExists: true) @@ -46,6 +47,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/beagle/target.22Jul22.46e.vcf.gz", checkIfExists: true) @@ -77,6 +79,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/beagle/target.22Jul22.46e.vcf.gz", checkIfExists: true) diff --git a/modules/nf-core/bedops/convert2bed/tests/main.nf.test b/modules/nf-core/bedops/convert2bed/tests/main.nf.test index 3f2b193a6d4..99fb8eead02 100644 --- a/modules/nf-core/bedops/convert2bed/tests/main.nf.test +++ b/modules/nf-core/bedops/convert2bed/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gtf', checkIfExists: true) @@ -39,6 +40,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gtf', checkIfExists: true) diff --git a/modules/nf-core/bedops/gtf2bed/tests/main.nf.test b/modules/nf-core/bedops/gtf2bed/tests/main.nf.test index c6f4ed22678..c4a6bb92939 100644 --- a/modules/nf-core/bedops/gtf2bed/tests/main.nf.test +++ b/modules/nf-core/bedops/gtf2bed/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [[ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] @@ -37,6 +38,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [[ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] diff --git a/modules/nf-core/bedtools/bamtobed/tests/main.nf.test b/modules/nf-core/bedtools/bamtobed/tests/main.nf.test index 297f1813362..7af82c6020b 100644 --- a/modules/nf-core/bedtools/bamtobed/tests/main.nf.test +++ b/modules/nf-core/bedtools/bamtobed/tests/main.nf.test @@ -11,7 +11,8 @@ nextflow_process { test("sarscov2 - bam") { when { process { - """ + """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.bam', checkIfExists: true) @@ -35,7 +36,8 @@ nextflow_process { when { process { - """ + """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.bam', checkIfExists: true) diff --git a/modules/nf-core/bedtools/closest/tests/main.nf.test b/modules/nf-core/bedtools/closest/tests/main.nf.test index f99ae18bad2..a4bd2d52321 100644 --- a/modules/nf-core/bedtools/closest/tests/main.nf.test +++ b/modules/nf-core/bedtools/closest/tests/main.nf.test @@ -11,7 +11,8 @@ nextflow_process { test("homo_sapiens") { when { process { - """ + """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true), @@ -37,7 +38,8 @@ nextflow_process { test("homo_sapiens - fai") { when { process { - """ + """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true), @@ -60,7 +62,8 @@ nextflow_process { test("homo_sapiens - vcf") { when { process { - """ + """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true), diff --git a/modules/nf-core/bedtools/complement/tests/main.nf.test b/modules/nf-core/bedtools/complement/tests/main.nf.test index b65c8fbf2f1..d249f35d526 100644 --- a/modules/nf-core/bedtools/complement/tests/main.nf.test +++ b/modules/nf-core/bedtools/complement/tests/main.nf.test @@ -11,7 +11,8 @@ nextflow_process { test("sarscov2") { when { process { - """ + """ + // testy mctestface input[0] = [ [ id:'test_out' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) diff --git a/modules/nf-core/bedtools/coverage/tests/main.nf.test b/modules/nf-core/bedtools/coverage/tests/main.nf.test index 57eb83dec1a..ad8d1afe6fb 100644 --- a/modules/nf-core/bedtools/coverage/tests/main.nf.test +++ b/modules/nf-core/bedtools/coverage/tests/main.nf.test @@ -12,7 +12,8 @@ nextflow_process { test("sarscov2") { when { process { - """ + """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true), @@ -35,7 +36,8 @@ nextflow_process { test("sarscov2 - fai") { when { process { - """ + """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true), diff --git a/modules/nf-core/bedtools/genomecov/tests/main.nf.test b/modules/nf-core/bedtools/genomecov/tests/main.nf.test index 16a03492c43..6b4ac4a437a 100644 --- a/modules/nf-core/bedtools/genomecov/tests/main.nf.test +++ b/modules/nf-core/bedtools/genomecov/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.bam", checkIfExists: true), @@ -39,6 +40,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.bam", checkIfExists: true), @@ -65,6 +67,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], file(params.modules_testdata_base_path + "genomics/sarscov2/genome/bed/baits.bed", checkIfExists: true), @@ -93,6 +96,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.bam", checkIfExists: true), @@ -121,6 +125,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.bam", checkIfExists: true), @@ -149,6 +154,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], file(params.modules_testdata_base_path + "genomics/sarscov2/genome/bed/baits.bed", checkIfExists: true), diff --git a/modules/nf-core/bedtools/getfasta/tests/main.nf.test b/modules/nf-core/bedtools/getfasta/tests/main.nf.test index 54ef4fc7ed0..118001a6ba6 100644 --- a/modules/nf-core/bedtools/getfasta/tests/main.nf.test +++ b/modules/nf-core/bedtools/getfasta/tests/main.nf.test @@ -13,7 +13,8 @@ nextflow_process { when { process { - """ + """ + // testy mctestface input[0] = [ [ id:'test', single_end:false], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true), @@ -39,7 +40,8 @@ nextflow_process { when { process { - """ + """ + // testy mctestface input[0] = [ [ id:'test', single_end:false], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true), diff --git a/modules/nf-core/bedtools/groupby/tests/main.nf.test b/modules/nf-core/bedtools/groupby/tests/main.nf.test index b7dedcc2aa5..b3c0b195d6f 100644 --- a/modules/nf-core/bedtools/groupby/tests/main.nf.test +++ b/modules/nf-core/bedtools/groupby/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true), diff --git a/modules/nf-core/bedtools/intersect/tests/main.nf.test b/modules/nf-core/bedtools/intersect/tests/main.nf.test index cd77094679d..8294b580254 100644 --- a/modules/nf-core/bedtools/intersect/tests/main.nf.test +++ b/modules/nf-core/bedtools/intersect/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true), @@ -40,6 +41,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true), @@ -67,6 +69,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true), diff --git a/modules/nf-core/bedtools/jaccard/tests/main.nf.test b/modules/nf-core/bedtools/jaccard/tests/main.nf.test index 839266b5fcc..8a80370626a 100644 --- a/modules/nf-core/bedtools/jaccard/tests/main.nf.test +++ b/modules/nf-core/bedtools/jaccard/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), @@ -41,6 +42,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), diff --git a/modules/nf-core/bedtools/makewindows/tests/main.nf.test b/modules/nf-core/bedtools/makewindows/tests/main.nf.test index b27e59b6e04..5c839b92936 100644 --- a/modules/nf-core/bedtools/makewindows/tests/main.nf.test +++ b/modules/nf-core/bedtools/makewindows/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test2'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) @@ -38,6 +39,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test2'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) diff --git a/modules/nf-core/bedtools/map/tests/main.nf.test b/modules/nf-core/bedtools/map/tests/main.nf.test index e46cf74377b..6ceb65d0aa6 100644 --- a/modules/nf-core/bedtools/map/tests/main.nf.test +++ b/modules/nf-core/bedtools/map/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true), @@ -40,6 +41,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true), @@ -65,6 +67,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true), diff --git a/modules/nf-core/bedtools/maskfasta/tests/main.nf.test b/modules/nf-core/bedtools/maskfasta/tests/main.nf.test index 14dfc33e31a..7bf6df7dbe9 100644 --- a/modules/nf-core/bedtools/maskfasta/tests/main.nf.test +++ b/modules/nf-core/bedtools/maskfasta/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) ] diff --git a/modules/nf-core/bedtools/merge/tests/main.nf.test b/modules/nf-core/bedtools/merge/tests/main.nf.test index 2959d6b9825..554e2d2276d 100644 --- a/modules/nf-core/bedtools/merge/tests/main.nf.test +++ b/modules/nf-core/bedtools/merge/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) ] diff --git a/modules/nf-core/bedtools/multiinter/tests/main.nf.test b/modules/nf-core/bedtools/multiinter/tests/main.nf.test index ed46cf0d3bc..e5d9c24f89e 100644 --- a/modules/nf-core/bedtools/multiinter/tests/main.nf.test +++ b/modules/nf-core/bedtools/multiinter/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ @@ -41,6 +42,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ diff --git a/modules/nf-core/bedtools/shift/tests/main.nf.test b/modules/nf-core/bedtools/shift/tests/main.nf.test index 5c251401aea..baeb9e54d89 100644 --- a/modules/nf-core/bedtools/shift/tests/main.nf.test +++ b/modules/nf-core/bedtools/shift/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) ] diff --git a/modules/nf-core/bedtools/slop/tests/main.nf.test b/modules/nf-core/bedtools/slop/tests/main.nf.test index c8dccc8e6ed..4e16841bf72 100644 --- a/modules/nf-core/bedtools/slop/tests/main.nf.test +++ b/modules/nf-core/bedtools/slop/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) ] diff --git a/modules/nf-core/bedtools/sort/tests/main.nf.test b/modules/nf-core/bedtools/sort/tests/main.nf.test index b1f36dd9197..ccfe226f19b 100644 --- a/modules/nf-core/bedtools/sort/tests/main.nf.test +++ b/modules/nf-core/bedtools/sort/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) ] @@ -38,6 +39,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) ] diff --git a/modules/nf-core/bedtools/split/tests/main.nf.test b/modules/nf-core/bedtools/split/tests/main.nf.test index a59891b7936..e727bdcecce 100644 --- a/modules/nf-core/bedtools/split/tests/main.nf.test +++ b/modules/nf-core/bedtools/split/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.multi_intervals.bed', checkIfExists: true), diff --git a/modules/nf-core/bedtools/subtract/tests/main.nf.test b/modules/nf-core/bedtools/subtract/tests/main.nf.test index cc4729c8bf2..9f51b3c4f8a 100644 --- a/modules/nf-core/bedtools/subtract/tests/main.nf.test +++ b/modules/nf-core/bedtools/subtract/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test_subtract' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/baits.bed', checkIfExists: true), diff --git a/modules/nf-core/bedtools/unionbedg/tests/main.nf.test b/modules/nf-core/bedtools/unionbedg/tests/main.nf.test index 8ae4d3e656d..d69ab696a70 100644 --- a/modules/nf-core/bedtools/unionbedg/tests/main.nf.test +++ b/modules/nf-core/bedtools/unionbedg/tests/main.nf.test @@ -13,7 +13,8 @@ nextflow_process { when { process { - """ + """ + // testy mctestface input[0] = [ [ id:'test_out' ], [ @@ -42,7 +43,8 @@ nextflow_process { when { process { - """ + """ + // testy mctestface input[0] = [ [ id:'test_out' ], [ @@ -74,7 +76,8 @@ nextflow_process { when { process { - """ + """ + // testy mctestface input[0] = [ [ id:'test_out' ], [ diff --git a/modules/nf-core/bioawk/tests/main.nf.test b/modules/nf-core/bioawk/tests/main.nf.test index 270ff1ef3ec..3a8e8919366 100644 --- a/modules/nf-core/bioawk/tests/main.nf.test +++ b/modules/nf-core/bioawk/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) diff --git a/modules/nf-core/biobambam/bammarkduplicates2/tests/main.nf.test b/modules/nf-core/biobambam/bammarkduplicates2/tests/main.nf.test index 954635ce801..27942658620 100644 --- a/modules/nf-core/biobambam/bammarkduplicates2/tests/main.nf.test +++ b/modules/nf-core/biobambam/bammarkduplicates2/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) @@ -43,6 +44,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) diff --git a/modules/nf-core/biobambam/bammerge/tests/main.nf.test b/modules/nf-core/biobambam/bammerge/tests/main.nf.test index 0316229b858..3676590e045 100644 --- a/modules/nf-core/biobambam/bammerge/tests/main.nf.test +++ b/modules/nf-core/biobambam/bammerge/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ @@ -47,6 +48,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ diff --git a/modules/nf-core/biobambam/bamsormadup/tests/main.nf.test b/modules/nf-core/biobambam/bamsormadup/tests/main.nf.test index 43272ff1604..452f0540efc 100644 --- a/modules/nf-core/biobambam/bamsormadup/tests/main.nf.test +++ b/modules/nf-core/biobambam/bamsormadup/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ @@ -48,6 +49,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ @@ -82,6 +84,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ diff --git a/modules/nf-core/biscuit/align/tests/main.nf.test b/modules/nf-core/biscuit/align/tests/main.nf.test index 1dc3eb3faca..157c292e011 100644 --- a/modules/nf-core/biscuit/align/tests/main.nf.test +++ b/modules/nf-core/biscuit/align/tests/main.nf.test @@ -26,6 +26,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test.methylated_1.fastq.gz', checkIfExists: true) ] @@ -50,6 +51,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test.methylated_1.fastq.gz', checkIfExists: true), diff --git a/modules/nf-core/biscuit/biscuitblaster/tests/main.nf.test b/modules/nf-core/biscuit/biscuitblaster/tests/main.nf.test index ccea7f5b85e..4580dcf2193 100644 --- a/modules/nf-core/biscuit/biscuitblaster/tests/main.nf.test +++ b/modules/nf-core/biscuit/biscuitblaster/tests/main.nf.test @@ -24,6 +24,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test.methylated_1.fastq.gz", checkIfExists: true) ] ] @@ -49,6 +50,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test.methylated_1.fastq.gz", checkIfExists: true), file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test.methylated_2.fastq.gz", checkIfExists: true) ] @@ -75,6 +77,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test.methylated_1.fastq.gz", checkIfExists: true), file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test.methylated_2.fastq.gz", checkIfExists: true) ] diff --git a/modules/nf-core/biscuit/bsconv/tests/main.nf.test b/modules/nf-core/biscuit/bsconv/tests/main.nf.test index 1cbf306a88b..673b73dd2e8 100644 --- a/modules/nf-core/biscuit/bsconv/tests/main.nf.test +++ b/modules/nf-core/biscuit/bsconv/tests/main.nf.test @@ -26,6 +26,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam.bai', checkIfExists: true) @@ -53,6 +54,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam.bai', checkIfExists: true) diff --git a/modules/nf-core/biscuit/epiread/tests/main.nf.test b/modules/nf-core/biscuit/epiread/tests/main.nf.test index 5a151008afa..c7f00f5eefd 100644 --- a/modules/nf-core/biscuit/epiread/tests/main.nf.test +++ b/modules/nf-core/biscuit/epiread/tests/main.nf.test @@ -26,6 +26,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam', checkIfExists: true), @@ -51,6 +52,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam', checkIfExists: true), @@ -76,6 +78,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam', checkIfExists: true), @@ -102,6 +105,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam', checkIfExists: true), diff --git a/modules/nf-core/biscuit/index/tests/main.nf.test b/modules/nf-core/biscuit/index/tests/main.nf.test index 0402a262200..fc623deaa7f 100644 --- a/modules/nf-core/biscuit/index/tests/main.nf.test +++ b/modules/nf-core/biscuit/index/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) """ @@ -35,6 +36,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) """ diff --git a/modules/nf-core/biscuit/mergecg/tests/main.nf.test b/modules/nf-core/biscuit/mergecg/tests/main.nf.test index 0b593f76842..31755cd07f8 100644 --- a/modules/nf-core/biscuit/mergecg/tests/main.nf.test +++ b/modules/nf-core/biscuit/mergecg/tests/main.nf.test @@ -24,6 +24,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + "delete_me/biscuit/test-cg.bed.gz", checkIfExists: true) @@ -58,6 +59,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + "delete_me/biscuit/test-cg.bed.gz", checkIfExists: true) diff --git a/modules/nf-core/biscuit/pileup/tests/main.nf.test b/modules/nf-core/biscuit/pileup/tests/main.nf.test index b188103a06f..6eca60cbade 100644 --- a/modules/nf-core/biscuit/pileup/tests/main.nf.test +++ b/modules/nf-core/biscuit/pileup/tests/main.nf.test @@ -26,6 +26,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ @@ -63,6 +64,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), @@ -95,6 +97,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), diff --git a/modules/nf-core/biscuit/qc/tests/main.nf.test b/modules/nf-core/biscuit/qc/tests/main.nf.test index d4b4e57ad47..27f457b1195 100644 --- a/modules/nf-core/biscuit/qc/tests/main.nf.test +++ b/modules/nf-core/biscuit/qc/tests/main.nf.test @@ -26,6 +26,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam', checkIfExists: true) @@ -50,6 +51,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam', checkIfExists: true) diff --git a/modules/nf-core/biscuit/vcf2bed/tests/main.nf.test b/modules/nf-core/biscuit/vcf2bed/tests/main.nf.test index 527f0c0ff4f..09781732e1e 100644 --- a/modules/nf-core/biscuit/vcf2bed/tests/main.nf.test +++ b/modules/nf-core/biscuit/vcf2bed/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/biscuit/test.vcf.gz', checkIfExists: true) @@ -38,6 +39,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/biscuit/test.vcf.gz', checkIfExists: true) diff --git a/modules/nf-core/bismark/coverage2cytosine/tests/main.nf.test b/modules/nf-core/bismark/coverage2cytosine/tests/main.nf.test index 3ed5c0d2d37..050af62f02d 100644 --- a/modules/nf-core/bismark/coverage2cytosine/tests/main.nf.test +++ b/modules/nf-core/bismark/coverage2cytosine/tests/main.nf.test @@ -39,6 +39,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = BISMARK_METHYLATIONEXTRACTOR.out.coverage input[1] = BISMARK_GENOMEPREPARATION.out.index """ diff --git a/modules/nf-core/bismark/methylationextractor/tests/main.nf.test b/modules/nf-core/bismark/methylationextractor/tests/main.nf.test index dea2c1fed8c..d0255a60fa7 100644 --- a/modules/nf-core/bismark/methylationextractor/tests/main.nf.test +++ b/modules/nf-core/bismark/methylationextractor/tests/main.nf.test @@ -25,6 +25,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.bam', checkIfExists: true) diff --git a/modules/nf-core/blast/makeblastdb/tests/main.nf.test b/modules/nf-core/blast/makeblastdb/tests/main.nf.test index 21caf1415cb..0728266e3b9 100644 --- a/modules/nf-core/blast/makeblastdb/tests/main.nf.test +++ b/modules/nf-core/blast/makeblastdb/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] """ } @@ -54,6 +55,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true) ] """ } diff --git a/modules/nf-core/blast/updateblastdb/tests/main.nf.test b/modules/nf-core/blast/updateblastdb/tests/main.nf.test index bf42c257d00..e75fa2f9c38 100644 --- a/modules/nf-core/blast/updateblastdb/tests/main.nf.test +++ b/modules/nf-core/blast/updateblastdb/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id:'test'], 'mito' ] """ } @@ -36,6 +37,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id:'test'], 'mito' ] """ } @@ -59,6 +61,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id:'test'], 'mito' ] """ } diff --git a/modules/nf-core/blat/tests/main.nf.test b/modules/nf-core/blat/tests/main.nf.test index 8b07e5cf72f..ef767b66d11 100644 --- a/modules/nf-core/blat/tests/main.nf.test +++ b/modules/nf-core/blat/tests/main.nf.test @@ -31,6 +31,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = SEQTK_SEQ.out.fastx input[1] = [ [ id:'sarscov2' ], @@ -54,6 +55,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = SEQTK_SEQ.out.fastx input[1] = [ [ id:'sarscov2' ], diff --git a/modules/nf-core/bowtie/align/tests/main.nf.test b/modules/nf-core/bowtie/align/tests/main.nf.test index 3403ae225fb..6dabae98d22 100644 --- a/modules/nf-core/bowtie/align/tests/main.nf.test +++ b/modules/nf-core/bowtie/align/tests/main.nf.test @@ -28,6 +28,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id:"test", single_end:true], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ] @@ -57,6 +58,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id:"test", single_end:true], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ] @@ -80,6 +82,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id:"test", single_end:false], [file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)] @@ -108,6 +111,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id:"test", single_end:false], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ] diff --git a/modules/nf-core/bowtie/build/tests/main.nf.test b/modules/nf-core/bowtie/build/tests/main.nf.test index b58f1d69a2f..edbfe9ed0a6 100644 --- a/modules/nf-core/bowtie/build/tests/main.nf.test +++ b/modules/nf-core/bowtie/build/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id: 'sarscov2'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) @@ -39,6 +40,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [[id: 'sarscov2'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] diff --git a/modules/nf-core/bowtie2/align/tests/main.nf.test b/modules/nf-core/bowtie2/align/tests/main.nf.test index 0de5950fee6..f7037f04fd0 100644 --- a/modules/nf-core/bowtie2/align/tests/main.nf.test +++ b/modules/nf-core/bowtie2/align/tests/main.nf.test @@ -28,6 +28,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) @@ -74,6 +75,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) @@ -120,6 +122,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) @@ -165,6 +168,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) @@ -210,6 +214,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ @@ -258,6 +263,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ @@ -307,6 +313,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) @@ -353,6 +360,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ @@ -401,6 +409,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ @@ -449,6 +458,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) @@ -496,6 +506,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ @@ -543,6 +554,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ @@ -593,6 +605,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) diff --git a/modules/nf-core/bowtie2/build/tests/main.nf.test b/modules/nf-core/bowtie2/build/tests/main.nf.test index 163760257a5..c20c267dae3 100644 --- a/modules/nf-core/bowtie2/build/tests/main.nf.test +++ b/modules/nf-core/bowtie2/build/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) diff --git a/modules/nf-core/bracken/bracken/tests/main.nf.test b/modules/nf-core/bracken/bracken/tests/main.nf.test index 9d2105dedb1..16bf6d0dc48 100644 --- a/modules/nf-core/bracken/bracken/tests/main.nf.test +++ b/modules/nf-core/bracken/bracken/tests/main.nf.test @@ -43,6 +43,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = KRAKEN2_KRAKEN2.out.report input[1] = UNTAR.out.untar.map{it[1]} """ @@ -85,6 +86,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = KRAKEN2_KRAKEN2.out.report input[1] = UNTAR.out.untar.map{it[1]} """ @@ -127,6 +129,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = KRAKEN2_KRAKEN2.out.report input[1] = UNTAR.out.untar.map{it[1]} """ @@ -149,6 +152,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [[id: 'test'],file(params.modules_testdata_base_path + 'generic/txt/hello.txt', checkIfExists: true)] input[1] = UNTAR.out.untar.map{it[1]} """ diff --git a/modules/nf-core/bracken/build/tests/main.nf.test b/modules/nf-core/bracken/build/tests/main.nf.test index 781c1518436..4f95df94af3 100644 --- a/modules/nf-core/bracken/build/tests/main.nf.test +++ b/modules/nf-core/bracken/build/tests/main.nf.test @@ -26,6 +26,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = UNTAR.out.untar """ } @@ -67,6 +68,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = UNTAR.out.untar """ } diff --git a/modules/nf-core/bracken/combinebrackenoutputs/tests/main.nf.test b/modules/nf-core/bracken/combinebrackenoutputs/tests/main.nf.test index e1504702156..91d5e31c1a5 100644 --- a/modules/nf-core/bracken/combinebrackenoutputs/tests/main.nf.test +++ b/modules/nf-core/bracken/combinebrackenoutputs/tests/main.nf.test @@ -60,6 +60,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = BRACKEN_BRACKEN.out.reports .map{it[1]} .collect() @@ -83,6 +84,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = BRACKEN_BRACKEN.out.reports .map{it[1]} .collect() diff --git a/modules/nf-core/busco/busco/tests/main.nf.test b/modules/nf-core/busco/busco/tests/main.nf.test index bb7b49a97c4..03fbb79475f 100644 --- a/modules/nf-core/busco/busco/tests/main.nf.test +++ b/modules/nf-core/busco/busco/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/genome/genome.fna.gz', checkIfExists: true) @@ -77,6 +78,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ @@ -163,6 +165,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) @@ -226,6 +229,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) @@ -269,6 +273,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/proteome.fasta', checkIfExists: true) @@ -331,6 +336,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/fasta/test1.contigs.fa.gz', checkIfExists: true) @@ -392,6 +398,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/genome/genome.fna.gz', checkIfExists: true) diff --git a/modules/nf-core/busco/generateplot/tests/main.nf.test b/modules/nf-core/busco/generateplot/tests/main.nf.test index 0bf1ff18990..e9e9199b660 100644 --- a/modules/nf-core/busco/generateplot/tests/main.nf.test +++ b/modules/nf-core/busco/generateplot/tests/main.nf.test @@ -33,6 +33,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = BUSCO_BUSCO.out.short_summaries_txt.map { meta, summary -> summary } """ } @@ -55,6 +56,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/genome/genome.fna.gz', checkIfExists: true) """ } diff --git a/modules/nf-core/bwa/aln/tests/main.nf.test b/modules/nf-core/bwa/aln/tests/main.nf.test index b290c5e76a7..d24800886ef 100644 --- a/modules/nf-core/bwa/aln/tests/main.nf.test +++ b/modules/nf-core/bwa/aln/tests/main.nf.test @@ -28,6 +28,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map [ @@ -67,6 +68,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ diff --git a/modules/nf-core/bwa/index/tests/main.nf.test b/modules/nf-core/bwa/index/tests/main.nf.test index af33e73ca12..39fb467fdc1 100644 --- a/modules/nf-core/bwa/index/tests/main.nf.test +++ b/modules/nf-core/bwa/index/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id: 'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) diff --git a/modules/nf-core/bwa/mem/tests/main.nf.test b/modules/nf-core/bwa/mem/tests/main.nf.test index 5de2c2f4539..463ba6bfcf1 100644 --- a/modules/nf-core/bwa/mem/tests/main.nf.test +++ b/modules/nf-core/bwa/mem/tests/main.nf.test @@ -28,6 +28,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map [ @@ -63,6 +64,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map [ @@ -98,6 +100,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ @@ -134,6 +137,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ @@ -170,6 +174,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ @@ -208,6 +213,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map [ @@ -236,6 +242,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ diff --git a/modules/nf-core/bwa/sampe/tests/main.nf.test b/modules/nf-core/bwa/sampe/tests/main.nf.test index 63a921f3838..89efdedc4ba 100644 --- a/modules/nf-core/bwa/sampe/tests/main.nf.test +++ b/modules/nf-core/bwa/sampe/tests/main.nf.test @@ -44,6 +44,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel .fromList( [ diff --git a/modules/nf-core/bwa/samse/tests/main.nf.test b/modules/nf-core/bwa/samse/tests/main.nf.test index 8a96ee4badc..7729962b578 100644 --- a/modules/nf-core/bwa/samse/tests/main.nf.test +++ b/modules/nf-core/bwa/samse/tests/main.nf.test @@ -41,6 +41,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel .fromList( [ diff --git a/modules/nf-core/bwamem2/index/tests/main.nf.test b/modules/nf-core/bwamem2/index/tests/main.nf.test index dbf11132c78..12d78e3cb2a 100644 --- a/modules/nf-core/bwamem2/index/tests/main.nf.test +++ b/modules/nf-core/bwamem2/index/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id: 'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) diff --git a/modules/nf-core/bwamem2/mem/tests/main.nf.test b/modules/nf-core/bwamem2/mem/tests/main.nf.test index 9e0ab14aec5..859942d880d 100644 --- a/modules/nf-core/bwamem2/mem/tests/main.nf.test +++ b/modules/nf-core/bwamem2/mem/tests/main.nf.test @@ -29,6 +29,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:true ], // meta map [file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)] @@ -58,6 +59,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:true ], // meta map [file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)] @@ -87,6 +89,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map [ @@ -119,6 +122,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map [ @@ -153,6 +157,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map [ diff --git a/modules/nf-core/bwameme/index/tests/main.nf.test b/modules/nf-core/bwameme/index/tests/main.nf.test index b61f7660d3d..1f49c721c51 100644 --- a/modules/nf-core/bwameme/index/tests/main.nf.test +++ b/modules/nf-core/bwameme/index/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id: 'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) @@ -39,6 +40,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id: 'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) diff --git a/modules/nf-core/bwameme/mem/tests/main.nf.test b/modules/nf-core/bwameme/mem/tests/main.nf.test index 6d93fd6ebfa..81f3ae3d5ba 100644 --- a/modules/nf-core/bwameme/mem/tests/main.nf.test +++ b/modules/nf-core/bwameme/mem/tests/main.nf.test @@ -31,6 +31,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:true ], // meta map [file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)] @@ -62,6 +63,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:true ], // meta map [file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)] @@ -93,6 +95,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map [ @@ -127,6 +130,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map [ @@ -163,6 +167,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map [ diff --git a/modules/nf-core/bwameth/align/tests/main.nf.test b/modules/nf-core/bwameth/align/tests/main.nf.test index 94b1f56fde6..5d000ee906d 100644 --- a/modules/nf-core/bwameth/align/tests/main.nf.test +++ b/modules/nf-core/bwameth/align/tests/main.nf.test @@ -28,6 +28,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map [ @@ -57,6 +58,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ @@ -88,6 +90,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ diff --git a/modules/nf-core/bwameth/index/tests/main.nf.test b/modules/nf-core/bwameth/index/tests/main.nf.test index a314788ab00..ae2006a4fae 100644 --- a/modules/nf-core/bwameth/index/tests/main.nf.test +++ b/modules/nf-core/bwameth/index/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) """ } diff --git a/modules/nf-core/cafe/tests/main.nf.test b/modules/nf-core/cafe/tests/main.nf.test index 312aea20130..ea832cb65c6 100644 --- a/modules/nf-core/cafe/tests/main.nf.test +++ b/modules/nf-core/cafe/tests/main.nf.test @@ -12,6 +12,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + "delete_me/cafe/hog_gene_counts.small.tsv", checkIfExists: true) ] @@ -41,6 +42,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + "delete_me/cafe/hog_gene_counts.small.tsv", checkIfExists: true) ] diff --git a/modules/nf-core/calder2/tests/main.nf.test b/modules/nf-core/calder2/tests/main.nf.test index 7833470e782..99fdcb58cc3 100644 --- a/modules/nf-core/calder2/tests/main.nf.test +++ b/modules/nf-core/calder2/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], //meta map file('https://raw.githubusercontent.com/CSOgroup/CALDER2/main/tests/testthat/data/test.cool', checkIfExists: true) @@ -64,6 +65,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], //meta map file('https://raw.githubusercontent.com/CSOgroup/CALDER2/main/tests/testthat/data/test.mcool', checkIfExists: true) @@ -113,6 +115,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], //meta map file('https://raw.githubusercontent.com/CSOgroup/CALDER2/main/tests/testthat/data/test.mcool', checkIfExists: true) diff --git a/modules/nf-core/cat/fastq/tests/main.nf.test b/modules/nf-core/cat/fastq/tests/main.nf.test index f88a78b6ca7..eb5328626d5 100644 --- a/modules/nf-core/cat/fastq/tests/main.nf.test +++ b/modules/nf-core/cat/fastq/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:true ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), @@ -37,6 +38,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), @@ -61,6 +63,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:true ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), @@ -83,6 +86,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), @@ -107,6 +111,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:true ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)] @@ -130,6 +135,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:true ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), @@ -154,6 +160,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), @@ -180,6 +187,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:true ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), @@ -204,6 +212,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), @@ -230,6 +239,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:true ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)] diff --git a/modules/nf-core/cdhit/cdhit/tests/main.nf.test b/modules/nf-core/cdhit/cdhit/tests/main.nf.test index 2daea9dd2ff..cdc4855c8ef 100644 --- a/modules/nf-core/cdhit/cdhit/tests/main.nf.test +++ b/modules/nf-core/cdhit/cdhit/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'proteomics/database/yeast_UPS.fasta', checkIfExists: true) diff --git a/modules/nf-core/cdhit/cdhitest/tests/main.nf.test b/modules/nf-core/cdhit/cdhitest/tests/main.nf.test index 509edadcf96..c797a720527 100644 --- a/modules/nf-core/cdhit/cdhitest/tests/main.nf.test +++ b/modules/nf-core/cdhit/cdhitest/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/contigs.fasta', checkIfExists: true) @@ -37,6 +38,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/contigs.fasta', checkIfExists: true) diff --git a/modules/nf-core/celesta/tests/main.nf.test b/modules/nf-core/celesta/tests/main.nf.test index 18fcd060f48..fd48fa50458 100644 --- a/modules/nf-core/celesta/tests/main.nf.test +++ b/modules/nf-core/celesta/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'imaging/downstream/celesta/img_data.csv', checkIfExists: true) @@ -46,6 +47,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], diff --git a/modules/nf-core/cellbender/merge/tests/main.nf.test b/modules/nf-core/cellbender/merge/tests/main.nf.test index e011fc45f1a..b0382c1cacc 100644 --- a/modules/nf-core/cellbender/merge/tests/main.nf.test +++ b/modules/nf-core/cellbender/merge/tests/main.nf.test @@ -12,6 +12,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file("https://raw.githubusercontent.com/nf-core/test-datasets/scdownstream/samples/SAMN14430799_custom_emptydrops_filter_matrix_5k.h5ad", checkIfExists: true), @@ -35,6 +36,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file("https://raw.githubusercontent.com/nf-core/test-datasets/scdownstream/samples/SAMN14430799_custom_emptydrops_filter_matrix_5k.h5ad", checkIfExists: true), diff --git a/modules/nf-core/cellbender/removebackground/tests/main.nf.test b/modules/nf-core/cellbender/removebackground/tests/main.nf.test index 1afa6f3bf00..9a9ca5b8893 100644 --- a/modules/nf-core/cellbender/removebackground/tests/main.nf.test +++ b/modules/nf-core/cellbender/removebackground/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file("https://raw.githubusercontent.com/nf-core/test-datasets/scdownstream/samples/SAMN14430799_raw_matrix_5k.h5ad", checkIfExists: true) @@ -41,6 +42,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file("https://raw.githubusercontent.com/nf-core/test-datasets/scdownstream/samples/SAMN14430799_raw_matrix_5k.h5ad", checkIfExists: true) diff --git a/modules/nf-core/cellpose/tests/main.nf.test b/modules/nf-core/cellpose/tests/main.nf.test index 6a7688baa8b..b2a353d2596 100644 --- a/modules/nf-core/cellpose/tests/main.nf.test +++ b/modules/nf-core/cellpose/tests/main.nf.test @@ -42,6 +42,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'imaging/segmentation/cycif_tonsil_registered.ome.tif', checkIfExists: true) diff --git a/modules/nf-core/cellranger/count/tests/main.nf.test b/modules/nf-core/cellranger/count/tests/main.nf.test index 3029c0ca5da..ec47cecf947 100644 --- a/modules/nf-core/cellranger/count/tests/main.nf.test +++ b/modules/nf-core/cellranger/count/tests/main.nf.test @@ -40,6 +40,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test_10x', single_end:false, strandedness:'auto' ], // meta map [ @@ -78,6 +79,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test_10x', single_end:false, strandedness:'auto' ], // meta map [ diff --git a/modules/nf-core/cellranger/mkfastq/tests/main.nf.test b/modules/nf-core/cellranger/mkfastq/tests/main.nf.test index 8d3d718f56b..0c43f156a0c 100644 --- a/modules/nf-core/cellranger/mkfastq/tests/main.nf.test +++ b/modules/nf-core/cellranger/mkfastq/tests/main.nf.test @@ -31,6 +31,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = UNTAR.out.untar.map{ it -> [ [ id: 'test', lane:1 ], file("https://cf.10xgenomics.com/supp/cell-exp/cellranger-tiny-bcl-simple-1.2.0.csv", checkIfExists: true), it[1] ] } """ } @@ -56,6 +57,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = UNTAR.out.untar.map{ it -> [ [ id: 'test', lane:1 ], file("https://cf.10xgenomics.com/supp/cell-exp/cellranger-tiny-bcl-samplesheet-1.2.0.csv", checkIfExists: true), it[1] ] } """ } @@ -83,6 +85,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = UNTAR.out.untar.map{ it -> [ [ id: 'test', lane:1 ], file("https://cf.10xgenomics.com/supp/cell-exp/cellranger-tiny-bcl-simple-1.2.0.csv", checkIfExists: true), it[1] ] } """ } diff --git a/modules/nf-core/cellranger/mkgtf/tests/main.nf.test b/modules/nf-core/cellranger/mkgtf/tests/main.nf.test index 8ede4df1b52..91b2ff72fa0 100644 --- a/modules/nf-core/cellranger/mkgtf/tests/main.nf.test +++ b/modules/nf-core/cellranger/mkgtf/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) """ } @@ -36,6 +37,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) """ } diff --git a/modules/nf-core/cellranger/mkref/tests/main.nf.test b/modules/nf-core/cellranger/mkref/tests/main.nf.test index dfbcd2220b0..cd9bb731d9b 100644 --- a/modules/nf-core/cellranger/mkref/tests/main.nf.test +++ b/modules/nf-core/cellranger/mkref/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) input[2] = "homo_sapiens_reference" @@ -52,6 +53,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [] input[1] = [] input[2] = "homo_sapiens_reference" diff --git a/modules/nf-core/cellranger/mkvdjref/tests/main.nf.test b/modules/nf-core/cellranger/mkvdjref/tests/main.nf.test index facb469b388..5daad6a6632 100644 --- a/modules/nf-core/cellranger/mkvdjref/tests/main.nf.test +++ b/modules/nf-core/cellranger/mkvdjref/tests/main.nf.test @@ -44,6 +44,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = GUNZIP_FASTA.out.gunzip.map{ it[1] } input[1] = GUNZIP_GTF.out.gunzip.map{ it[1] } input[2] = [] @@ -68,6 +69,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [] input[1] = [] input[2] = [] diff --git a/modules/nf-core/cellranger/multi/tests/main.nf.test b/modules/nf-core/cellranger/multi/tests/main.nf.test index 0259e1b3548..df8be6e5669 100644 --- a/modules/nf-core/cellranger/multi/tests/main.nf.test +++ b/modules/nf-core/cellranger/multi/tests/main.nf.test @@ -42,6 +42,7 @@ nextflow_process { when { process { """ + // testy mctestface // // preparation // @@ -252,6 +253,7 @@ nextflow_process { when { process { """ + // testy mctestface // // preparation: unfortunately have to repeat data load // @@ -492,6 +494,7 @@ nextflow_process { when { process { """ + // testy mctestface // // preparation: unfortunately have to repeat data load // diff --git a/modules/nf-core/cellranger/vdj/tests/main.nf.test b/modules/nf-core/cellranger/vdj/tests/main.nf.test index 7a8df889a68..bea06bd4bd6 100644 --- a/modules/nf-core/cellranger/vdj/tests/main.nf.test +++ b/modules/nf-core/cellranger/vdj/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface reference_json = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/10xgenomics/cellranger/references/vdj/refdata-cellranger-vdj-GRCh38-alts-ensembl-5.0.0/reference.json', checkIfExists: true) reference_fasta = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/10xgenomics/cellranger/references/vdj/refdata-cellranger-vdj-GRCh38-alts-ensembl-5.0.0/fasta/regions.fa', checkIfExists: true) reference_suppfasta = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/10xgenomics/cellranger/references/vdj/refdata-cellranger-vdj-GRCh38-alts-ensembl-5.0.0/fasta/supp_regions.fa', checkIfExists: true) @@ -57,6 +58,7 @@ nextflow_process { when { process { """ + // testy mctestface reference_json = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/10xgenomics/cellranger/references/vdj/refdata-cellranger-vdj-GRCh38-alts-ensembl-5.0.0/reference.json', checkIfExists: true) reference_fasta = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/10xgenomics/cellranger/references/vdj/refdata-cellranger-vdj-GRCh38-alts-ensembl-5.0.0/fasta/regions.fa', checkIfExists: true) reference_suppfasta = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/10xgenomics/cellranger/references/vdj/refdata-cellranger-vdj-GRCh38-alts-ensembl-5.0.0/fasta/supp_regions.fa', checkIfExists: true) diff --git a/modules/nf-core/cellrangerarc/mkgtf/tests/main.nf.test b/modules/nf-core/cellrangerarc/mkgtf/tests/main.nf.test index 1a386af0642..589d15d9064 100644 --- a/modules/nf-core/cellrangerarc/mkgtf/tests/main.nf.test +++ b/modules/nf-core/cellrangerarc/mkgtf/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = file(params.modules_testdata_base_path + 'genomics/mus_musculus/genome/chr19.filtered.gtf.gz', checkIfExists: true) """ @@ -36,6 +37,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = file(params.modules_testdata_base_path + 'genomics/mus_musculus/genome/chr19.filtered.gtf.gz', checkIfExists: true) """ diff --git a/modules/nf-core/cellsnp/modea/tests/main.nf.test b/modules/nf-core/cellsnp/modea/tests/main.nf.test index 8f67d265153..a8bdb8b5472 100644 --- a/modules/nf-core/cellsnp/modea/tests/main.nf.test +++ b/modules/nf-core/cellsnp/modea/tests/main.nf.test @@ -27,7 +27,8 @@ nextflow_process { when { process { - """ + """ + // testy mctestface input[0] = SAMTOOLS_INDEX.out.bai.collect{ meta, bai -> bai }.map{ bai -> [[ id: 'sample1'], @@ -62,6 +63,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'sample1'], diff --git a/modules/nf-core/centrifuge/build/tests/main.nf.test b/modules/nf-core/centrifuge/build/tests/main.nf.test index 07d584fd461..d70621d4353 100644 --- a/modules/nf-core/centrifuge/build/tests/main.nf.test +++ b/modules/nf-core/centrifuge/build/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id: 'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/metagenome/seqid2taxid.map', checkIfExists: true) input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/metagenome/nodes.dmp', checkIfExists: true) @@ -38,6 +39,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id: 'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/metagenome/seqid2taxid.map', checkIfExists: true) input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/metagenome/nodes.dmp', checkIfExists: true) diff --git a/modules/nf-core/centrifuge/centrifuge/tests/main.nf.test b/modules/nf-core/centrifuge/centrifuge/tests/main.nf.test index f2713608572..46cd2aab2e0 100644 --- a/modules/nf-core/centrifuge/centrifuge/tests/main.nf.test +++ b/modules/nf-core/centrifuge/centrifuge/tests/main.nf.test @@ -26,6 +26,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id: 'test', single_end: true], file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ] input[1] = UNTAR.out.untar.map{ it[1] } input[2] = true @@ -53,6 +54,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), @@ -86,6 +88,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id: 'test'], file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ] input[1] = UNTAR.out.untar.map{ it[1] } input[2] = true diff --git a/modules/nf-core/centrifuge/kreport/tests/main.nf.test b/modules/nf-core/centrifuge/kreport/tests/main.nf.test index 6d4bc6b1d2a..e99cae8a5a8 100644 --- a/modules/nf-core/centrifuge/kreport/tests/main.nf.test +++ b/modules/nf-core/centrifuge/kreport/tests/main.nf.test @@ -39,6 +39,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = CENTRIFUGE_CENTRIFUGE.out.results input[1] = UNTAR.out.untar.map{it[1]} """ @@ -64,6 +65,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = CENTRIFUGE_CENTRIFUGE.out.results input[1] = UNTAR.out.untar.map{it[1]} """ diff --git a/modules/nf-core/checkm/lineagewf/tests/main.nf.test b/modules/nf-core/checkm/lineagewf/tests/main.nf.test index 28dfb46f363..755142e7b0e 100644 --- a/modules/nf-core/checkm/lineagewf/tests/main.nf.test +++ b/modules/nf-core/checkm/lineagewf/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/contigs.fasta', checkIfExists: true) diff --git a/modules/nf-core/checkm2/databasedownload/tests/main.nf.test b/modules/nf-core/checkm2/databasedownload/tests/main.nf.test index 2a98f0510ce..08c3394cbbc 100644 --- a/modules/nf-core/checkm2/databasedownload/tests/main.nf.test +++ b/modules/nf-core/checkm2/databasedownload/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [] """ } diff --git a/modules/nf-core/checkqc/tests/main.nf.test b/modules/nf-core/checkqc/tests/main.nf.test index c780f9c08b2..3bf70dc84b6 100644 --- a/modules/nf-core/checkqc/tests/main.nf.test +++ b/modules/nf-core/checkqc/tests/main.nf.test @@ -25,6 +25,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = UNTAR.out.untar input[1] = [] """ @@ -61,6 +62,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = UNTAR.out.untar input[1] = [] """ @@ -92,6 +94,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = UNTAR.out.untar input[1] = [] """ diff --git a/modules/nf-core/checkv/endtoend/tests/main.nf.test b/modules/nf-core/checkv/endtoend/tests/main.nf.test index c3b6718cd42..1d2a7eae158 100644 --- a/modules/nf-core/checkv/endtoend/tests/main.nf.test +++ b/modules/nf-core/checkv/endtoend/tests/main.nf.test @@ -46,6 +46,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = GUNZIP.out.gunzip input[1] = UNTAR.out.untar.map { it[1] } """ @@ -70,6 +71,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = GUNZIP.out.gunzip input[1] = UNTAR.out.untar.map { it[1] } """ diff --git a/modules/nf-core/checkv/updatedatabase/tests/main.nf.test b/modules/nf-core/checkv/updatedatabase/tests/main.nf.test index 5a82c80e539..84bd0d38ae2 100644 --- a/modules/nf-core/checkv/updatedatabase/tests/main.nf.test +++ b/modules/nf-core/checkv/updatedatabase/tests/main.nf.test @@ -71,6 +71,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of( [ [ id: 'test' ], diff --git a/modules/nf-core/chewbbaca/createschema/tests/main.nf.test b/modules/nf-core/chewbbaca/createschema/tests/main.nf.test index 0cac4c3fb0f..e71dd9364d6 100644 --- a/modules/nf-core/chewbbaca/createschema/tests/main.nf.test +++ b/modules/nf-core/chewbbaca/createschema/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/contigs.fasta', checkIfExists: true) @@ -40,6 +41,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/contigs.fasta', checkIfExists: true), @@ -67,6 +69,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/contigs.fasta', checkIfExists: true), @@ -96,6 +99,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/contigs.fasta', checkIfExists: true), diff --git a/modules/nf-core/chromap/chromap/tests/main.nf.test b/modules/nf-core/chromap/chromap/tests/main.nf.test index a20382f9bef..917f13b95fb 100644 --- a/modules/nf-core/chromap/chromap/tests/main.nf.test +++ b/modules/nf-core/chromap/chromap/tests/main.nf.test @@ -32,6 +32,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) @@ -62,6 +63,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ @@ -141,6 +143,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) diff --git a/modules/nf-core/chromap/index/tests/main.nf.test b/modules/nf-core/chromap/index/tests/main.nf.test index 619e085bbd9..35abcb25711 100644 --- a/modules/nf-core/chromap/index/tests/main.nf.test +++ b/modules/nf-core/chromap/index/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) @@ -40,6 +41,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) diff --git a/modules/nf-core/chromograph/tests/main.nf.test b/modules/nf-core/chromograph/tests/main.nf.test index 8643afe3a6d..fa39d50d5ba 100644 --- a/modules/nf-core/chromograph/tests/main.nf.test +++ b/modules/nf-core/chromograph/tests/main.nf.test @@ -12,6 +12,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [[:],[]] input[1] = [[:],[]] input[2] = [[:],[]] diff --git a/modules/nf-core/circexplorer2/annotate/tests/main.nf.test b/modules/nf-core/circexplorer2/annotate/tests/main.nf.test index 3ad614a4f27..af900d98423 100644 --- a/modules/nf-core/circexplorer2/annotate/tests/main.nf.test +++ b/modules/nf-core/circexplorer2/annotate/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'fust1_3' ], file("https://raw.githubusercontent.com/nf-core/test-datasets/circrna/circexplorer2/fust1_3.junction.bed") @@ -47,6 +48,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'fust1_3' ], file("https://raw.githubusercontent.com/nf-core/test-datasets/circrna/circexplorer2/fust1_3.junction.bed") diff --git a/modules/nf-core/circexplorer2/parse/tests/main.nf.test b/modules/nf-core/circexplorer2/parse/tests/main.nf.test index 4768ab5ddbc..e04a382208c 100644 --- a/modules/nf-core/circexplorer2/parse/tests/main.nf.test +++ b/modules/nf-core/circexplorer2/parse/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'fust1_3' ], file("https://raw.githubusercontent.com/nf-core/test-datasets/circrna/circexplorer2/fust1_3.Chimeric.out.junction") @@ -42,6 +43,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'fust1_3' ], file("https://raw.githubusercontent.com/nf-core/test-datasets/circrna/circexplorer2/fust1_3.Chimeric.out.junction") diff --git a/modules/nf-core/circularmapper/circulargenerator/tests/main.nf.test b/modules/nf-core/circularmapper/circulargenerator/tests/main.nf.test index b95471884b9..70b1a2f8f0b 100644 --- a/modules/nf-core/circularmapper/circulargenerator/tests/main.nf.test +++ b/modules/nf-core/circularmapper/circulargenerator/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) @@ -39,6 +40,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) diff --git a/modules/nf-core/circularmapper/realignsamfile/tests/main.nf.test b/modules/nf-core/circularmapper/realignsamfile/tests/main.nf.test index 2ec30b73f7a..e572176c6c7 100644 --- a/modules/nf-core/circularmapper/realignsamfile/tests/main.nf.test +++ b/modules/nf-core/circularmapper/realignsamfile/tests/main.nf.test @@ -72,6 +72,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = BWA_SAMSE.out.bam input[1] = [ [ id:'test' ], // meta map @@ -99,6 +100,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id: "test" ], //meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.bam', checkIfExists: true) diff --git a/modules/nf-core/clame/tests/main.nf.test b/modules/nf-core/clame/tests/main.nf.test index a11c74f2dda..27120380866 100644 --- a/modules/nf-core/clame/tests/main.nf.test +++ b/modules/nf-core/clame/tests/main.nf.test @@ -28,6 +28,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = GUNZIP.out.gunzip """ } @@ -49,6 +50,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = GUNZIP.out.gunzip """ } diff --git a/modules/nf-core/clonalframeml/tests/main.nf.test b/modules/nf-core/clonalframeml/tests/main.nf.test index 15a1154c945..e2b18e0ba09 100644 --- a/modules/nf-core/clonalframeml/tests/main.nf.test +++ b/modules/nf-core/clonalframeml/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/prokaryotes/haemophilus_influenzae/genome/genome.aln.nwk', checkIfExists: true), diff --git a/modules/nf-core/clustalo/align/tests/main.nf.test b/modules/nf-core/clustalo/align/tests/main.nf.test index 6e20610e1ae..eb774753122 100644 --- a/modules/nf-core/clustalo/align/tests/main.nf.test +++ b/modules/nf-core/clustalo/align/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/contigs.fasta', checkIfExists: true) ] @@ -40,6 +41,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/contigs.fasta', checkIfExists: true) ] @@ -78,6 +80,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/contigs.fasta', checkIfExists: true) ] diff --git a/modules/nf-core/clustalo/guidetree/tests/main.nf.test b/modules/nf-core/clustalo/guidetree/tests/main.nf.test index 67bdeb7ed2f..9e8faf60dda 100644 --- a/modules/nf-core/clustalo/guidetree/tests/main.nf.test +++ b/modules/nf-core/clustalo/guidetree/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/contigs.fasta', checkIfExists: true) ] diff --git a/modules/nf-core/cmseq/polymut/tests/main.nf.test b/modules/nf-core/cmseq/polymut/tests/main.nf.test index ab34f70b376..f86490c73d0 100644 --- a/modules/nf-core/cmseq/polymut/tests/main.nf.test +++ b/modules/nf-core/cmseq/polymut/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), @@ -40,6 +41,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), @@ -65,6 +67,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), @@ -91,6 +94,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), diff --git a/modules/nf-core/cnvkit/access/tests/main.nf.test b/modules/nf-core/cnvkit/access/tests/main.nf.test index 63bf79f1dee..3c60cd5422c 100644 --- a/modules/nf-core/cnvkit/access/tests/main.nf.test +++ b/modules/nf-core/cnvkit/access/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id: "test" ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true) @@ -41,6 +42,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id: "test" ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true) @@ -67,6 +69,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id: "test" ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true) diff --git a/modules/nf-core/cnvkit/antitarget/tests/main.nf.test b/modules/nf-core/cnvkit/antitarget/tests/main.nf.test index 84f3818007f..d464f651dbb 100644 --- a/modules/nf-core/cnvkit/antitarget/tests/main.nf.test +++ b/modules/nf-core/cnvkit/antitarget/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id: 'test'], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed', checkIfExists: true) @@ -38,6 +39,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id: 'test'], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed', checkIfExists: true) diff --git a/modules/nf-core/cnvkit/batch/tests/main.nf.test b/modules/nf-core/cnvkit/batch/tests/main.nf.test index f191a4b952c..c2ef23b6729 100644 --- a/modules/nf-core/cnvkit/batch/tests/main.nf.test +++ b/modules/nf-core/cnvkit/batch/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), @@ -47,6 +48,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam', checkIfExists: true), @@ -77,6 +79,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test2.paired_end.sorted.cram', checkIfExists: true), @@ -107,6 +110,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam', checkIfExists: true), @@ -137,6 +141,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test2.paired_end.recalibrated.sorted.cram', checkIfExists: true), @@ -165,6 +170,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], // meta map [], @@ -194,6 +200,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), @@ -225,6 +232,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], // meta map [], @@ -259,6 +267,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), diff --git a/modules/nf-core/cnvkit/call/tests/main.nf.test b/modules/nf-core/cnvkit/call/tests/main.nf.test index 6012ef137f7..6beb1d8454f 100644 --- a/modules/nf-core/cnvkit/call/tests/main.nf.test +++ b/modules/nf-core/cnvkit/call/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file('https://raw.githubusercontent.com/etal/cnvkit/v0.9.9/test/formats/amplicon.cns', checkIfExists: true), @@ -38,6 +39,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file('https://raw.githubusercontent.com/etal/cnvkit/v0.9.9/test/formats/amplicon.cns', checkIfExists: true), @@ -62,6 +64,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file('https://raw.githubusercontent.com/etal/cnvkit/v0.9.9/test/formats/amplicon.cns', checkIfExists: true), diff --git a/modules/nf-core/cnvkit/genemetrics/tests/main.nf.test b/modules/nf-core/cnvkit/genemetrics/tests/main.nf.test index a2d8b4580cf..127aadd3d80 100644 --- a/modules/nf-core/cnvkit/genemetrics/tests/main.nf.test +++ b/modules/nf-core/cnvkit/genemetrics/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file('https://raw.githubusercontent.com/etal/cnvkit/v0.9.9/test/formats/amplicon.cnr', checkIfExists: true), @@ -38,6 +39,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file('https://raw.githubusercontent.com/etal/cnvkit/v0.9.9/test/formats/amplicon.cnr', checkIfExists: true), diff --git a/modules/nf-core/cnvkit/reference/tests/main.nf.test b/modules/nf-core/cnvkit/reference/tests/main.nf.test index f03dd231f3a..e1a0aca2ef5 100644 --- a/modules/nf-core/cnvkit/reference/tests/main.nf.test +++ b/modules/nf-core/cnvkit/reference/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true) input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed', checkIfExists: true) input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.antitarget.bed', checkIfExists: true) @@ -37,6 +38,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true) input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed', checkIfExists: true) input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.antitarget.bed', checkIfExists: true) diff --git a/modules/nf-core/cnvkit/target/tests/main.nf.test b/modules/nf-core/cnvkit/target/tests/main.nf.test index fb2161a2db9..13833233fb4 100644 --- a/modules/nf-core/cnvkit/target/tests/main.nf.test +++ b/modules/nf-core/cnvkit/target/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true) @@ -38,6 +39,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true) @@ -65,6 +67,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true) diff --git a/modules/nf-core/cnvpytor/callcnvs/tests/main.nf.test b/modules/nf-core/cnvpytor/callcnvs/tests/main.nf.test index f6dd8da5195..5bd513b6fd0 100644 --- a/modules/nf-core/cnvpytor/callcnvs/tests/main.nf.test +++ b/modules/nf-core/cnvpytor/callcnvs/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/pytor/test.pytor', checkIfExists: true) @@ -38,6 +39,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/pytor/test.pytor', checkIfExists: true) diff --git a/modules/nf-core/cnvpytor/importreaddepth/tests/main.nf.test b/modules/nf-core/cnvpytor/importreaddepth/tests/main.nf.test index 316afecb149..7ce17b571b7 100644 --- a/modules/nf-core/cnvpytor/importreaddepth/tests/main.nf.test +++ b/modules/nf-core/cnvpytor/importreaddepth/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id: 'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam', checkIfExists: true), @@ -45,6 +46,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id: 'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), @@ -74,6 +76,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id: 'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), diff --git a/modules/nf-core/cnvpytor/view/tests/main.nf.test b/modules/nf-core/cnvpytor/view/tests/main.nf.test index 2d6f9fb49bd..5e480adbeb8 100644 --- a/modules/nf-core/cnvpytor/view/tests/main.nf.test +++ b/modules/nf-core/cnvpytor/view/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], // meta map [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/pytor/test.pytor', checkIfExists: true) ] @@ -40,6 +41,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], // meta map [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/pytor/test.pytor', checkIfExists: true) ] @@ -68,6 +70,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], // meta map [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/pytor/test.pytor', checkIfExists: true) ] diff --git a/modules/nf-core/cobs/classicconstruct/tests/main.nf.test b/modules/nf-core/cobs/classicconstruct/tests/main.nf.test index 5c172d3244e..1a0cf1a3c97 100644 --- a/modules/nf-core/cobs/classicconstruct/tests/main.nf.test +++ b/modules/nf-core/cobs/classicconstruct/tests/main.nf.test @@ -12,6 +12,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) @@ -32,6 +33,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) diff --git a/modules/nf-core/cobs/compactconstruct/tests/main.nf.test b/modules/nf-core/cobs/compactconstruct/tests/main.nf.test index 75df99c4f8c..a984c160bda 100644 --- a/modules/nf-core/cobs/compactconstruct/tests/main.nf.test +++ b/modules/nf-core/cobs/compactconstruct/tests/main.nf.test @@ -12,6 +12,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) @@ -32,6 +33,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) diff --git a/modules/nf-core/concoct/concoct/tests/main.nf.test b/modules/nf-core/concoct/concoct/tests/main.nf.test index a979ebe37ce..c7b80e883b5 100644 --- a/modules/nf-core/concoct/concoct/tests/main.nf.test +++ b/modules/nf-core/concoct/concoct/tests/main.nf.test @@ -56,6 +56,7 @@ nextflow_process { when { process { """ + // testy mctestface ch_input_for_concoctconcoct = CONCOCT_CONCOCTCOVERAGETABLE.out.tsv .join(CONCOCT_CUTUPFASTA.out.fasta) @@ -88,6 +89,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id: 'test'], [], [] ] """ } diff --git a/modules/nf-core/concoct/concoctcoveragetable/tests/main.nf.test b/modules/nf-core/concoct/concoctcoveragetable/tests/main.nf.test index dc378b52d43..5f96f75b0b1 100644 --- a/modules/nf-core/concoct/concoctcoveragetable/tests/main.nf.test +++ b/modules/nf-core/concoct/concoctcoveragetable/tests/main.nf.test @@ -30,6 +30,7 @@ nextflow_process { when { process { """ + // testy mctestface ch_bam_input = Channel .fromList([ [ @@ -67,6 +68,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id:'test'], [], [] ,[] ] """ } diff --git a/modules/nf-core/concoct/cutupfasta/tests/main.nf.test b/modules/nf-core/concoct/cutupfasta/tests/main.nf.test index 0c395ee2381..05394873ab3 100644 --- a/modules/nf-core/concoct/cutupfasta/tests/main.nf.test +++ b/modules/nf-core/concoct/cutupfasta/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id: 'test', single_end: false], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) @@ -39,6 +40,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id: 'test', single_end: false], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) diff --git a/modules/nf-core/concoct/extractfastabins/tests/main.nf.test b/modules/nf-core/concoct/extractfastabins/tests/main.nf.test index ce14d726dad..8e885a51a0f 100644 --- a/modules/nf-core/concoct/extractfastabins/tests/main.nf.test +++ b/modules/nf-core/concoct/extractfastabins/tests/main.nf.test @@ -78,6 +78,7 @@ nextflow_process { when { process { """ + // testy mctestface fasta = [ [id: 'test', single_end: false], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) @@ -103,6 +104,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id: 'test', single_end: false], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true), diff --git a/modules/nf-core/concoct/mergecutupclustering/tests/main.nf.test b/modules/nf-core/concoct/mergecutupclustering/tests/main.nf.test index b888c2fadc9..1751c2e2d80 100644 --- a/modules/nf-core/concoct/mergecutupclustering/tests/main.nf.test +++ b/modules/nf-core/concoct/mergecutupclustering/tests/main.nf.test @@ -69,6 +69,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = CONCOCT_CONCOCT.out.clustering_csv """ } @@ -90,6 +91,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id: 'test'], []] """ } diff --git a/modules/nf-core/controlfreec/assesssignificance/tests/main.nf.test b/modules/nf-core/controlfreec/assesssignificance/tests/main.nf.test index b44e3b36ab4..e8ebd4e7008 100644 --- a/modules/nf-core/controlfreec/assesssignificance/tests/main.nf.test +++ b/modules/nf-core/controlfreec/assesssignificance/tests/main.nf.test @@ -64,6 +64,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = CONTROLFREEC_FREEC.out.CNV.join(CONTROLFREEC_FREEC.out.ratio) """ } @@ -142,6 +143,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = CONTROLFREEC_FREEC.out.CNV.join(CONTROLFREEC_FREEC.out.ratio) """ } diff --git a/modules/nf-core/controlfreec/freec/tests/main.nf.test b/modules/nf-core/controlfreec/freec/tests/main.nf.test index 8e38becdfdc..c3bd17d8b51 100644 --- a/modules/nf-core/controlfreec/freec/tests/main.nf.test +++ b/modules/nf-core/controlfreec/freec/tests/main.nf.test @@ -31,6 +31,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false, sex:'XX' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/mpileup/test.mpileup.gz', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/mpileup/test2.mpileup.gz', checkIfExists: true), @@ -126,6 +127,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false, sex:'XX' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/mpileup/test.mpileup.gz', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/mpileup/test2.mpileup.gz', checkIfExists: true), diff --git a/modules/nf-core/controlfreec/freec2bed/tests/main.nf.test b/modules/nf-core/controlfreec/freec2bed/tests/main.nf.test index a2ad4b2f95b..dbf1a4e266c 100644 --- a/modules/nf-core/controlfreec/freec2bed/tests/main.nf.test +++ b/modules/nf-core/controlfreec/freec2bed/tests/main.nf.test @@ -63,6 +63,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = CONTROLFREEC_FREEC.out.ratio """ } @@ -140,6 +141,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = CONTROLFREEC_FREEC.out.ratio """ } diff --git a/modules/nf-core/controlfreec/freec2circos/tests/main.nf.test b/modules/nf-core/controlfreec/freec2circos/tests/main.nf.test index 2eb5936ad9b..7969be2ad07 100644 --- a/modules/nf-core/controlfreec/freec2circos/tests/main.nf.test +++ b/modules/nf-core/controlfreec/freec2circos/tests/main.nf.test @@ -63,6 +63,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = CONTROLFREEC_FREEC.out.ratio """ } @@ -141,6 +142,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = CONTROLFREEC_FREEC.out.ratio """ } diff --git a/modules/nf-core/controlfreec/makegraph/tests/main.nf.test b/modules/nf-core/controlfreec/makegraph/tests/main.nf.test index da2b218b69d..3256c58da2c 100644 --- a/modules/nf-core/controlfreec/makegraph/tests/main.nf.test +++ b/modules/nf-core/controlfreec/makegraph/tests/main.nf.test @@ -68,6 +68,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = CONTROLFREEC_FREEC.out.ratio.join(CONTROLFREEC_FREEC.out.BAF).combine(Channel.value("2")) """ } @@ -180,6 +181,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], [], [], [] diff --git a/modules/nf-core/controlfreec/makegraph2/tests/main.nf.test b/modules/nf-core/controlfreec/makegraph2/tests/main.nf.test index aed63f02aa6..4eba993b12e 100644 --- a/modules/nf-core/controlfreec/makegraph2/tests/main.nf.test +++ b/modules/nf-core/controlfreec/makegraph2/tests/main.nf.test @@ -64,6 +64,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = CONTROLFREEC_FREEC.out.ratio.join(CONTROLFREEC_FREEC.out.BAF) """ } @@ -141,6 +142,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], [], [] diff --git a/modules/nf-core/cooler/digest/tests/main.nf.test b/modules/nf-core/cooler/digest/tests/main.nf.test index c919f36a3c4..001c3123cb5 100644 --- a/modules/nf-core/cooler/digest/tests/main.nf.test +++ b/modules/nf-core/cooler/digest/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.sizes', checkIfExists: true) input[2] = "CviQI" diff --git a/modules/nf-core/cooler/dump/tests/main.nf.test b/modules/nf-core/cooler/dump/tests/main.nf.test index fc5a2249e41..6a1c60b0248 100644 --- a/modules/nf-core/cooler/dump/tests/main.nf.test +++ b/modules/nf-core/cooler/dump/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file("https://raw.githubusercontent.com/open2c/cooler/master/tests/data/toy.asymm.16.cool", checkIfExists: true), @@ -39,6 +40,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file("https://raw.githubusercontent.com/open2c/cooler/master/tests/data/toy.asymm.16.cool", checkIfExists: true), diff --git a/modules/nf-core/cooler/makebins/tests/main.nf.test b/modules/nf-core/cooler/makebins/tests/main.nf.test index 8a779304792..fbb2d62bcde 100644 --- a/modules/nf-core/cooler/makebins/tests/main.nf.test +++ b/modules/nf-core/cooler/makebins/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/cooler/cload/hg19/hg19.chrom.sizes', checkIfExists: true), diff --git a/modules/nf-core/crabz/compress/tests/main.nf.test b/modules/nf-core/crabz/compress/tests/main.nf.test index 8e34809c849..b7e8cc2ca5a 100644 --- a/modules/nf-core/crabz/compress/tests/main.nf.test +++ b/modules/nf-core/crabz/compress/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], // meta map @@ -40,6 +41,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], // meta map diff --git a/modules/nf-core/crabz/decompress/tests/main.nf.test b/modules/nf-core/crabz/decompress/tests/main.nf.test index 00dc01dfb6d..6c4527371bd 100644 --- a/modules/nf-core/crabz/decompress/tests/main.nf.test +++ b/modules/nf-core/crabz/decompress/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map @@ -41,6 +42,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map diff --git a/modules/nf-core/crumble/tests/main.nf.test b/modules/nf-core/crumble/tests/main.nf.test index ee520a4a00b..68840cdb4ba 100644 --- a/modules/nf-core/crumble/tests/main.nf.test +++ b/modules/nf-core/crumble/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) @@ -46,6 +47,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) @@ -78,6 +80,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) diff --git a/modules/nf-core/csvtk/concat/tests/main.nf.test b/modules/nf-core/csvtk/concat/tests/main.nf.test index 13f201475c5..277cbee5980 100644 --- a/modules/nf-core/csvtk/concat/tests/main.nf.test +++ b/modules/nf-core/csvtk/concat/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ file("https://github.com/nf-core/test-datasets/raw/bacass/bacass_hybrid.csv", checkIfExists: true), @@ -43,6 +44,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ file("https://github.com/nf-core/test-datasets/raw/bacass/bacass_hybrid.csv", checkIfExists: true), diff --git a/modules/nf-core/csvtk/join/tests/main.nf.test b/modules/nf-core/csvtk/join/tests/main.nf.test index 3cf178c4f95..5af0bd87fef 100644 --- a/modules/nf-core/csvtk/join/tests/main.nf.test +++ b/modules/nf-core/csvtk/join/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ @@ -41,6 +42,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ diff --git a/modules/nf-core/csvtk/split/tests/main.nf.test b/modules/nf-core/csvtk/split/tests/main.nf.test index f3c49926677..9367cbf36fa 100644 --- a/modules/nf-core/csvtk/split/tests/main.nf.test +++ b/modules/nf-core/csvtk/split/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ file(params.modules_testdata_base_path + '/generic/tsv/test.tsv', checkIfExists: true) ] @@ -40,6 +41,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ file(params.modules_testdata_base_path + '/generic/tsv/test.tsv', checkIfExists: true) ] diff --git a/modules/nf-core/custom/catadditionalfasta/tests/main.nf.test b/modules/nf-core/custom/catadditionalfasta/tests/main.nf.test index a0ef5c91d62..8fecaa217fb 100644 --- a/modules/nf-core/custom/catadditionalfasta/tests/main.nf.test +++ b/modules/nf-core/custom/catadditionalfasta/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true), diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test index b1e1630bb38..0d34b931a94 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test +++ b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface def tool1_version = ''' TOOL1: tool1: 0.11.9 diff --git a/modules/nf-core/custom/getchromsizes/tests/main.nf.test b/modules/nf-core/custom/getchromsizes/tests/main.nf.test index 2f741a4bbed..87ce1a8dc2e 100644 --- a/modules/nf-core/custom/getchromsizes/tests/main.nf.test +++ b/modules/nf-core/custom/getchromsizes/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) @@ -35,6 +36,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true) @@ -58,6 +60,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) @@ -81,6 +84,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true) diff --git a/modules/nf-core/custom/gtffilter/tests/main.nf.test b/modules/nf-core/custom/gtffilter/tests/main.nf.test index 252d11a1635..d5f9b5567fd 100644 --- a/modules/nf-core/custom/gtffilter/tests/main.nf.test +++ b/modules/nf-core/custom/gtffilter/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gtf', checkIfExists: true) @@ -39,6 +40,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gtf', checkIfExists: true) @@ -66,6 +68,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gtf', checkIfExists: true) @@ -93,6 +96,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gtf', checkIfExists: true) diff --git a/modules/nf-core/custom/tx2gene/tests/main.nf.test b/modules/nf-core/custom/tx2gene/tests/main.nf.test index 4cbb8d4efb4..3d377dddfdc 100644 --- a/modules/nf-core/custom/tx2gene/tests/main.nf.test +++ b/modules/nf-core/custom/tx2gene/tests/main.nf.test @@ -29,6 +29,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test'], // meta map file(params.modules_testdata_base_path + 'genomics/eukaryotes/saccharomyces_cerevisiae/genome_gfp.gtf', checkIfExists: true) @@ -70,6 +71,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test'], // meta map file(params.modules_testdata_base_path + 'genomics/eukaryotes/saccharomyces_cerevisiae/genome_gfp.gtf', checkIfExists: true) diff --git a/modules/nf-core/datavzrd/tests/main.nf.test b/modules/nf-core/datavzrd/tests/main.nf.test index 86bd849a0cf..3aef4858b58 100644 --- a/modules/nf-core/datavzrd/tests/main.nf.test +++ b/modules/nf-core/datavzrd/tests/main.nf.test @@ -11,6 +11,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id: "csv_config"], file(params.modules_testdata_base_path + 'generic/config/config_test.datavzrd.yaml', checkIfExists: true), file(params.modules_testdata_base_path + 'generic/csv/test.csv', checkIfExists: true) @@ -39,6 +40,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id: "tsv_config"], file(params.modules_testdata_base_path + 'generic/config/config_network.datavzrd.yaml', checkIfExists: true), file(params.modules_testdata_base_path + 'generic/tsv/network.tsv', checkIfExists: true) @@ -69,6 +71,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id: "csv_config"], file(params.modules_testdata_base_path + 'generic/config/config_test.datavzrd.yaml', checkIfExists: true), file(params.modules_testdata_base_path + 'generic/csv/test.csv', checkIfExists: true) @@ -89,6 +92,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [] """ } diff --git a/modules/nf-core/decoupler/decoupler/tests/main.nf.test b/modules/nf-core/decoupler/decoupler/tests/main.nf.test index 921ac3254e7..2120bcdd355 100644 --- a/modules/nf-core/decoupler/decoupler/tests/main.nf.test +++ b/modules/nf-core/decoupler/decoupler/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id: 'test' ], file(params.test_data['generic']['tsv']['expression'], checkIfExists: true) diff --git a/modules/nf-core/deeparg/downloaddata/tests/main.nf.test b/modules/nf-core/deeparg/downloaddata/tests/main.nf.test index 8e8c7647684..60a34365a3a 100644 --- a/modules/nf-core/deeparg/downloaddata/tests/main.nf.test +++ b/modules/nf-core/deeparg/downloaddata/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface // No input required """ } @@ -39,6 +40,7 @@ nextflow_process { when { process { """ + // testy mctestface // No input required """ } diff --git a/modules/nf-core/deeparg/predict/tests/main.nf.test b/modules/nf-core/deeparg/predict/tests/main.nf.test index 4841c6eb489..bdb3f220d1b 100644 --- a/modules/nf-core/deeparg/predict/tests/main.nf.test +++ b/modules/nf-core/deeparg/predict/tests/main.nf.test @@ -27,6 +27,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/genome/genome.fna.gz', checkIfExists: true), @@ -59,6 +60,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/genome/genome.fna.gz', checkIfExists: true), diff --git a/modules/nf-core/deepbgc/download/tests/main.nf.test b/modules/nf-core/deepbgc/download/tests/main.nf.test index a1c2c53255e..e414ac089e0 100644 --- a/modules/nf-core/deepbgc/download/tests/main.nf.test +++ b/modules/nf-core/deepbgc/download/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface """ } diff --git a/modules/nf-core/deepbgc/pipeline/tests/main.nf.test b/modules/nf-core/deepbgc/pipeline/tests/main.nf.test index 9dd24049e77..04444a6bc14 100644 --- a/modules/nf-core/deepbgc/pipeline/tests/main.nf.test +++ b/modules/nf-core/deepbgc/pipeline/tests/main.nf.test @@ -47,6 +47,7 @@ nextflow_process { when { process { """ + // testy mctestface input [0] = PRODIGAL.out.gene_annotations input [1] = DEEPBGC_DOWNLOAD.out.db """ @@ -71,6 +72,7 @@ nextflow_process { when { process { """ + // testy mctestface input [0] = GUNZIP.out.gunzip input [1] = DEEPBGC_DOWNLOAD.out.db """ @@ -98,6 +100,7 @@ nextflow_process { when { process { """ + // testy mctestface input [0] = GUNZIP.out.gunzip input [1] = DEEPBGC_DOWNLOAD.out.db """ diff --git a/modules/nf-core/deepcell/mesmer/tests/main.nf.test b/modules/nf-core/deepcell/mesmer/tests/main.nf.test index d960a548ae9..9e2bd25f6de 100644 --- a/modules/nf-core/deepcell/mesmer/tests/main.nf.test +++ b/modules/nf-core/deepcell/mesmer/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id: 'test_img' ], file(params.modules_testdata_base_path + 'imaging/segmentation/cycif_tonsil_registered.ome.tif', checkIfExists: true) diff --git a/modules/nf-core/deeptools/alignmentsieve/tests/main.nf.test b/modules/nf-core/deeptools/alignmentsieve/tests/main.nf.test index 2d3b61b93d8..62c8ba8bbb8 100644 --- a/modules/nf-core/deeptools/alignmentsieve/tests/main.nf.test +++ b/modules/nf-core/deeptools/alignmentsieve/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), @@ -41,6 +42,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), diff --git a/modules/nf-core/deeptools/bamcoverage/tests/main.nf.test b/modules/nf-core/deeptools/bamcoverage/tests/main.nf.test index 5d6978035ef..8cc08e36ff9 100644 --- a/modules/nf-core/deeptools/bamcoverage/tests/main.nf.test +++ b/modules/nf-core/deeptools/bamcoverage/tests/main.nf.test @@ -13,7 +13,8 @@ nextflow_process { when { process { - """ + """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), @@ -40,7 +41,8 @@ nextflow_process { when { process { - """ + """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), @@ -67,7 +69,8 @@ nextflow_process { when { process { - """ + """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), @@ -96,7 +99,8 @@ nextflow_process { when { process { - """ + """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), diff --git a/modules/nf-core/deeptools/computematrix/tests/main.nf.test b/modules/nf-core/deeptools/computematrix/tests/main.nf.test index 39873aa36d5..a95e4ae1332 100644 --- a/modules/nf-core/deeptools/computematrix/tests/main.nf.test +++ b/modules/nf-core/deeptools/computematrix/tests/main.nf.test @@ -14,7 +14,8 @@ nextflow_process { when { process { - """ + """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina//bigwig/test.bigwig', checkIfExists: true) @@ -46,6 +47,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina//bigwig/test.bigwig', checkIfExists: true) diff --git a/modules/nf-core/deeptools/multibamsummary/tests/main.nf.test b/modules/nf-core/deeptools/multibamsummary/tests/main.nf.test index a7093985370..4dca12c6206 100644 --- a/modules/nf-core/deeptools/multibamsummary/tests/main.nf.test +++ b/modules/nf-core/deeptools/multibamsummary/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ @@ -49,6 +50,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ diff --git a/modules/nf-core/deeptools/plotcorrelation/tests/main.nf.test b/modules/nf-core/deeptools/plotcorrelation/tests/main.nf.test index fcdc5c1e9b4..64e19e2b2f5 100644 --- a/modules/nf-core/deeptools/plotcorrelation/tests/main.nf.test +++ b/modules/nf-core/deeptools/plotcorrelation/tests/main.nf.test @@ -37,6 +37,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = DEEPTOOLS_MULTIBAMSUMMARY.out.matrix.collect{ meta, matrix -> matrix }.map{ matrix -> [[ id: 'test' ], matrix] } input[1] = 'spearman' input[2] = 'heatmap' @@ -83,6 +84,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = DEEPTOOLS_MULTIBAMSUMMARY.out.matrix.collect{ meta, matrix -> matrix }.map{ matrix -> [[ id: 'test' ], matrix] } input[1] = '' input[2] = 'heatmap' @@ -129,6 +131,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = DEEPTOOLS_MULTIBAMSUMMARY.out.matrix.collect{ meta, matrix -> matrix }.map{ matrix -> [[ id: 'test' ], matrix] } input[1] = 'spearman' input[2] = '' @@ -177,6 +180,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = DEEPTOOLS_MULTIBAMSUMMARY.out.matrix.collect{ meta, matrix -> matrix }.map{ matrix -> [[ id: 'test' ], matrix] } input[1] = 'spearman' input[2] = 'heatmap' diff --git a/modules/nf-core/deeptools/plotfingerprint/tests/main.nf.test b/modules/nf-core/deeptools/plotfingerprint/tests/main.nf.test index 818c6c9f4a2..55f701fb1fc 100644 --- a/modules/nf-core/deeptools/plotfingerprint/tests/main.nf.test +++ b/modules/nf-core/deeptools/plotfingerprint/tests/main.nf.test @@ -13,7 +13,8 @@ nextflow_process { when { process { - """ + """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), @@ -42,7 +43,8 @@ nextflow_process { when { process { - """ + """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), diff --git a/modules/nf-core/deeptools/plotheatmap/tests/main.nf.test b/modules/nf-core/deeptools/plotheatmap/tests/main.nf.test index b0bcaa9c735..197a84674d7 100644 --- a/modules/nf-core/deeptools/plotheatmap/tests/main.nf.test +++ b/modules/nf-core/deeptools/plotheatmap/tests/main.nf.test @@ -13,7 +13,8 @@ nextflow_process { when { process { - """ + """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/deeptools/test.computeMatrix.mat.gz', checkIfExists: true), @@ -42,6 +43,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/deeptools/test.computeMatrix.mat.gz', checkIfExists: true), diff --git a/modules/nf-core/deeptools/plotpca/tests/main.nf.test b/modules/nf-core/deeptools/plotpca/tests/main.nf.test index 7374bacf833..63db5ba0327 100644 --- a/modules/nf-core/deeptools/plotpca/tests/main.nf.test +++ b/modules/nf-core/deeptools/plotpca/tests/main.nf.test @@ -37,6 +37,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = DEEPTOOLS_MULTIBAMSUMMARY.out.matrix.collect{ meta, matrix -> matrix }.map{ matrix -> [[ id: 'test' ], matrix] } """ } @@ -83,6 +84,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = DEEPTOOLS_MULTIBAMSUMMARY.out.matrix.collect{ meta, matrix -> matrix }.map{ matrix -> [[ id: 'test' ], matrix] } """ } diff --git a/modules/nf-core/deeptools/plotprofile/tests/main.nf.test b/modules/nf-core/deeptools/plotprofile/tests/main.nf.test index fe52873b3e8..97626334e34 100644 --- a/modules/nf-core/deeptools/plotprofile/tests/main.nf.test +++ b/modules/nf-core/deeptools/plotprofile/tests/main.nf.test @@ -13,7 +13,8 @@ nextflow_process { when { process { - """ + """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/deeptools/test.computeMatrix.mat.gz', checkIfExists: true), @@ -42,6 +43,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/deeptools/test.computeMatrix.mat.gz', checkIfExists: true), diff --git a/modules/nf-core/deepvariant/callvariants/tests/main.nf.test b/modules/nf-core/deepvariant/callvariants/tests/main.nf.test index 72f04b51f3b..d72e44fa819 100644 --- a/modules/nf-core/deepvariant/callvariants/tests/main.nf.test +++ b/modules/nf-core/deepvariant/callvariants/tests/main.nf.test @@ -44,6 +44,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = DEEPVARIANT_MAKEEXAMPLES.out.examples """ } @@ -66,6 +67,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta [] // No input paths are needed in stub mode diff --git a/modules/nf-core/deepvariant/makeexamples/tests/main.nf.test b/modules/nf-core/deepvariant/makeexamples/tests/main.nf.test index d46dbe6d57c..eb8302e905a 100644 --- a/modules/nf-core/deepvariant/makeexamples/tests/main.nf.test +++ b/modules/nf-core/deepvariant/makeexamples/tests/main.nf.test @@ -69,6 +69,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), diff --git a/modules/nf-core/deepvariant/postprocessvariants/tests/main.nf.test b/modules/nf-core/deepvariant/postprocessvariants/tests/main.nf.test index e4e9b5570c2..936a90b389c 100644 --- a/modules/nf-core/deepvariant/postprocessvariants/tests/main.nf.test +++ b/modules/nf-core/deepvariant/postprocessvariants/tests/main.nf.test @@ -53,6 +53,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = DEEPVARIANT_CALLVARIANTS.out.call_variants_tfrecords.join( DEEPVARIANT_MAKEEXAMPLES.out.gvcf, failOnMismatch: true @@ -86,6 +87,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], [], diff --git a/modules/nf-core/deepvariant/rundeepvariant/tests/main.nf.test b/modules/nf-core/deepvariant/rundeepvariant/tests/main.nf.test index 0790fb81362..5106f292bbf 100644 --- a/modules/nf-core/deepvariant/rundeepvariant/tests/main.nf.test +++ b/modules/nf-core/deepvariant/rundeepvariant/tests/main.nf.test @@ -53,6 +53,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), @@ -91,6 +92,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), diff --git a/modules/nf-core/deepvariant/tests/main.nf.test b/modules/nf-core/deepvariant/tests/main.nf.test index cf62430fa5a..81f573d4e4d 100644 --- a/modules/nf-core/deepvariant/tests/main.nf.test +++ b/modules/nf-core/deepvariant/tests/main.nf.test @@ -12,6 +12,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), diff --git a/modules/nf-core/delly/call/tests/main.nf.test b/modules/nf-core/delly/call/tests/main.nf.test index 80cad20d553..51aa554bbf7 100644 --- a/modules/nf-core/delly/call/tests/main.nf.test +++ b/modules/nf-core/delly/call/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], // meta map file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam", checkIfExists:true), @@ -50,6 +51,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], // meta map file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/cram/test2.paired_end.recalibrated.sorted.cram", checkIfExists:true), @@ -84,6 +86,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], // meta map file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/cram/test2.paired_end.recalibrated.sorted.cram", checkIfExists:true), @@ -118,6 +121,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], // meta map file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/cram/test2.paired_end.recalibrated.sorted.cram", checkIfExists:true), @@ -155,6 +159,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], // meta map file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam", checkIfExists:true), diff --git a/modules/nf-core/demuxem/tests/main.nf.test b/modules/nf-core/demuxem/tests/main.nf.test index 49b75f70a8c..0f46af0a8ac 100644 --- a/modules/nf-core/demuxem/tests/main.nf.test +++ b/modules/nf-core/demuxem/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'sample1'], @@ -47,6 +48,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'sample1'], diff --git a/modules/nf-core/deseq2/differential/tests/main.nf.test b/modules/nf-core/deseq2/differential/tests/main.nf.test index 370f05dcd74..c0e90d13d46 100644 --- a/modules/nf-core/deseq2/differential/tests/main.nf.test +++ b/modules/nf-core/deseq2/differential/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface expression_test_data_dir = params.modules_testdata_base_path + 'genomics/mus_musculus/rnaseq_expression/' ch_contrasts = Channel.fromPath(file(expression_test_data_dir + 'SRP254919.contrasts.csv', checkIfExists: true)) @@ -64,6 +65,7 @@ nextflow_process { when { process { """ + // testy mctestface expression_test_data_dir = params.modules_testdata_base_path + 'genomics/mus_musculus/rnaseq_expression/' ch_contrasts = Channel.fromPath(file(expression_test_data_dir + 'SRP254919.contrasts.csv', checkIfExists: true)) @@ -118,6 +120,7 @@ nextflow_process { when { process { """ + // testy mctestface expression_test_data_dir = params.modules_testdata_base_path + 'genomics/mus_musculus/rnaseq_expression/' ch_contrasts = Channel.fromPath(file(expression_test_data_dir + 'SRP254919.contrasts.csv', checkIfExists: true)) @@ -166,6 +169,7 @@ nextflow_process { when { process { """ + // testy mctestface expression_test_data_dir = params.modules_testdata_base_path + 'genomics/mus_musculus/rnaseq_expression/' ch_contrasts = Channel.fromPath(file(expression_test_data_dir + 'SRP254919.contrasts.csv', checkIfExists: true)) @@ -217,6 +221,7 @@ nextflow_process { when { process { """ + // testy mctestface expression_test_data_dir = params.modules_testdata_base_path + 'genomics/mus_musculus/rnaseq_expression/' ch_contrasts = Channel.fromPath(file(expression_test_data_dir + 'SRP254919.contrasts.csv', checkIfExists: true)) @@ -268,6 +273,7 @@ nextflow_process { when { process { """ + // testy mctestface expression_test_data_dir = params.modules_testdata_base_path + 'genomics/mus_musculus/rnaseq_expression/' ch_contrasts = Channel.fromPath(file(expression_test_data_dir + 'SRP254919.contrasts.csv', checkIfExists: true)) @@ -322,6 +328,7 @@ nextflow_process { when { process { """ + // testy mctestface expression_test_data_dir = params.modules_testdata_base_path + 'genomics/mus_musculus/rnaseq_expression/' ch_contrasts = Channel.fromPath(file(expression_test_data_dir + 'SRP254919.contrasts.csv', checkIfExists: true)) @@ -370,6 +377,7 @@ nextflow_process { when { process { """ + // testy mctestface expression_test_data_dir = params.modules_testdata_base_path + 'genomics/mus_musculus/rnaseq_expression/' ch_contrasts = Channel.fromPath(file(expression_test_data_dir + 'SRP254919.contrasts.csv', checkIfExists: true)) @@ -418,6 +426,7 @@ nextflow_process { when { process { """ + // testy mctestface expression_test_data_dir = params.modules_testdata_base_path + 'genomics/mus_musculus/rnaseq_expression/' ch_contrasts = Channel.fromPath(file(expression_test_data_dir + 'SRP254919.contrasts.csv', checkIfExists: true)) @@ -467,6 +476,7 @@ nextflow_process { when { process { """ + // testy mctestface expression_test_data_dir = params.modules_testdata_base_path + 'genomics/mus_musculus/rnaseq_expression/' ch_contrasts = Channel.fromPath(file(expression_test_data_dir + 'SRP254919.contrasts.csv', checkIfExists: true)) diff --git a/modules/nf-core/diamond/cluster/tests/main.nf.test b/modules/nf-core/diamond/cluster/tests/main.nf.test index 198a7d458e5..77aed4b72e7 100644 --- a/modules/nf-core/diamond/cluster/tests/main.nf.test +++ b/modules/nf-core/diamond/cluster/tests/main.nf.test @@ -12,7 +12,8 @@ nextflow_process { test("human - fasta") { when { process { - """ + """ + // testy mctestface input[0] = [ [ id:'human' ], // meta map file(params.modules_testdata_base_path + 'proteomics/database/UP000005640_9606.fasta', checkIfExists: true) @@ -32,7 +33,8 @@ nextflow_process { test("human - dmnd") { when { process { - """ + """ + // testy mctestface input[0] = [ [ id:'human' ], // meta map file(params.modules_testdata_base_path + 'proteomics/database/UP000005640_9606.dmnd', checkIfExists: true) @@ -56,6 +58,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'proteomics/database/UP000005640_9606.fasta', checkIfExists: true) diff --git a/modules/nf-core/dragmap/align/tests/main.nf.test b/modules/nf-core/dragmap/align/tests/main.nf.test index d688c291c13..df732ac5bd0 100644 --- a/modules/nf-core/dragmap/align/tests/main.nf.test +++ b/modules/nf-core/dragmap/align/tests/main.nf.test @@ -28,6 +28,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) @@ -71,6 +72,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) @@ -114,6 +116,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ @@ -160,6 +163,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ @@ -206,6 +210,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ @@ -253,6 +258,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ diff --git a/modules/nf-core/dshbio/exportsegments/tests/main.nf.test b/modules/nf-core/dshbio/exportsegments/tests/main.nf.test index 8cc99183960..76e33b38006 100644 --- a/modules/nf-core/dshbio/exportsegments/tests/main.nf.test +++ b/modules/nf-core/dshbio/exportsegments/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ @@ -39,6 +40,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test_bgz' ], // meta map [ @@ -63,6 +65,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test_gz' ], // meta map [ @@ -87,6 +90,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test_zst' ], // meta map [ diff --git a/modules/nf-core/dshbio/filterbed/tests/main.nf.test b/modules/nf-core/dshbio/filterbed/tests/main.nf.test index 030cf8d6604..5462d53e232 100644 --- a/modules/nf-core/dshbio/filterbed/tests/main.nf.test +++ b/modules/nf-core/dshbio/filterbed/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) ] @@ -39,6 +40,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) ] diff --git a/modules/nf-core/dshbio/filtergff3/tests/main.nf.test b/modules/nf-core/dshbio/filtergff3/tests/main.nf.test index 83414e46ac9..93ab4b24209 100644 --- a/modules/nf-core/dshbio/filtergff3/tests/main.nf.test +++ b/modules/nf-core/dshbio/filtergff3/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ diff --git a/modules/nf-core/dshbio/splitbed/tests/main.nf.test b/modules/nf-core/dshbio/splitbed/tests/main.nf.test index 6d66cd44528..0be8350de72 100644 --- a/modules/nf-core/dshbio/splitbed/tests/main.nf.test +++ b/modules/nf-core/dshbio/splitbed/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) ] @@ -39,6 +40,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) ] diff --git a/modules/nf-core/dshbio/splitgff3/tests/main.nf.test b/modules/nf-core/dshbio/splitgff3/tests/main.nf.test index f24924b4c21..09ff5590596 100644 --- a/modules/nf-core/dshbio/splitgff3/tests/main.nf.test +++ b/modules/nf-core/dshbio/splitgff3/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gff3.gz', checkIfExists: true) ] ] @@ -38,6 +39,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gff3.gz', checkIfExists: true) ] ] diff --git a/modules/nf-core/dupradar/tests/main.nf.test b/modules/nf-core/dupradar/tests/main.nf.test index ef213df9fb6..0a7cc818751 100644 --- a/modules/nf-core/dupradar/tests/main.nf.test +++ b/modules/nf-core/dupradar/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true, strandedness:'forward' ], // meta map file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.single_end.bam", checkIfExists: true) @@ -52,6 +53,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true, strandedness:'forward' ], // meta map file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.single_end.bam", checkIfExists: true) @@ -79,6 +81,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false, strandedness:'forward' ], // meta map file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.bam", checkIfExists: true) @@ -116,6 +119,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false, strandedness:'forward' ], // meta map file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.bam", checkIfExists: true) diff --git a/modules/nf-core/dysgu/tests/main.nf.test b/modules/nf-core/dysgu/tests/main.nf.test index 1714b5b7ab3..9b1a2847236 100644 --- a/modules/nf-core/dysgu/tests/main.nf.test +++ b/modules/nf-core/dysgu/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam.bai', checkIfExists: true) @@ -42,6 +43,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram.crai', checkIfExists: true) @@ -72,6 +74,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam.bai', checkIfExists: true) diff --git a/modules/nf-core/ectyper/tests/main.nf.test b/modules/nf-core/ectyper/tests/main.nf.test index f1b962bb730..b3907d124ee 100644 --- a/modules/nf-core/ectyper/tests/main.nf.test +++ b/modules/nf-core/ectyper/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) diff --git a/modules/nf-core/eido/convert/tests/main.nf.test b/modules/nf-core/eido/convert/tests/main.nf.test index 51ac502fc8e..5a10d0a8479 100644 --- a/modules/nf-core/eido/convert/tests/main.nf.test +++ b/modules/nf-core/eido/convert/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/pep/test_nextflow_original_samplesheet.csv", checkIfExists: true) input[1] = "csv" input[2] = [] @@ -37,6 +38,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/pep/test_pep_format_files/config.yaml", checkIfExists: true) input[1] = "csv" input[2] = [] @@ -59,6 +61,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/pep/test_pep_format_files/config.yaml", checkIfExists: true) input[1] = "csv" input[2] = [] diff --git a/modules/nf-core/eido/validate/tests/main.nf.test b/modules/nf-core/eido/validate/tests/main.nf.test index 7cbbbf5de77..b8c86f4fa16 100644 --- a/modules/nf-core/eido/validate/tests/main.nf.test +++ b/modules/nf-core/eido/validate/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/pep/test_nextflow_original_samplesheet.csv", checkIfExists: true) input[1] = file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/pep/test_samplesheet_schema.yaml", checkIfExists: true) input[2] = [] @@ -41,6 +42,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/pep/test_pep_format_files/config.yaml", checkIfExists: true) input[1] = file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/pep/test_samplesheet_schema.yaml", checkIfExists: true) input[2] = [] diff --git a/modules/nf-core/eklipse/tests/main.nf.test b/modules/nf-core/eklipse/tests/main.nf.test index fb0be6d43c2..b5e7e3a8814 100644 --- a/modules/nf-core/eklipse/tests/main.nf.test +++ b/modules/nf-core/eklipse/tests/main.nf.test @@ -12,6 +12,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test_illumina_mt.bam', checkIfExists: true), diff --git a/modules/nf-core/elprep/filter/tests/main.nf.test b/modules/nf-core/elprep/filter/tests/main.nf.test index 413bff1a5a8..5dbf37bbe40 100644 --- a/modules/nf-core/elprep/filter/tests/main.nf.test +++ b/modules/nf-core/elprep/filter/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) @@ -61,6 +62,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) diff --git a/modules/nf-core/elprep/split/tests/main.nf.test b/modules/nf-core/elprep/split/tests/main.nf.test index 31a1725aeca..f44e1d0d496 100644 --- a/modules/nf-core/elprep/split/tests/main.nf.test +++ b/modules/nf-core/elprep/split/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) @@ -43,6 +44,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) diff --git a/modules/nf-core/emboss/cons/tests/main.nf.test b/modules/nf-core/emboss/cons/tests/main.nf.test index 7c7818fd08a..69be61b838a 100644 --- a/modules/nf-core/emboss/cons/tests/main.nf.test +++ b/modules/nf-core/emboss/cons/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/all_sites.fas', checkIfExists: true) @@ -37,6 +38,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/all_sites.fas', checkIfExists: true) diff --git a/modules/nf-core/emboss/revseq/tests/main.nf.test b/modules/nf-core/emboss/revseq/tests/main.nf.test index b8f980ea6db..3803713c3f5 100644 --- a/modules/nf-core/emboss/revseq/tests/main.nf.test +++ b/modules/nf-core/emboss/revseq/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) @@ -37,6 +38,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) diff --git a/modules/nf-core/emmtyper/tests/main.nf.test b/modules/nf-core/emmtyper/tests/main.nf.test index 12884647c8a..ddd958f2d7a 100644 --- a/modules/nf-core/emmtyper/tests/main.nf.test +++ b/modules/nf-core/emmtyper/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] diff --git a/modules/nf-core/ensemblvep/download/tests/main.nf.test b/modules/nf-core/ensemblvep/download/tests/main.nf.test index ac41cc3f325..4c1488cd1bf 100644 --- a/modules/nf-core/ensemblvep/download/tests/main.nf.test +++ b/modules/nf-core/ensemblvep/download/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [id:"112_WBcel235"], params.vep_genome, @@ -40,6 +41,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [id:"112_WBcel235"], params.vep_genome, diff --git a/modules/nf-core/ensemblvep/filtervep/tests/main.nf.test b/modules/nf-core/ensemblvep/filtervep/tests/main.nf.test index 1852e2ab7e2..ed3565c15da 100644 --- a/modules/nf-core/ensemblvep/filtervep/tests/main.nf.test +++ b/modules/nf-core/ensemblvep/filtervep/tests/main.nf.test @@ -58,6 +58,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = ENSEMBLVEP_VEP.out.vcf input[1] = [] """ @@ -119,6 +120,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = ENSEMBLVEP_VEP.out.tab input[1] = [] """ diff --git a/modules/nf-core/ensemblvep/vep/tests/main.nf.test b/modules/nf-core/ensemblvep/vep/tests/main.nf.test index e68fff3c0ea..4882d64f37e 100644 --- a/modules/nf-core/ensemblvep/vep/tests/main.nf.test +++ b/modules/nf-core/ensemblvep/vep/tests/main.nf.test @@ -34,6 +34,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true), @@ -85,6 +86,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true), diff --git a/modules/nf-core/entrezdirect/esummary/tests/main.nf.test b/modules/nf-core/entrezdirect/esummary/tests/main.nf.test index 6578a96cbef..a79fc4545df 100644 --- a/modules/nf-core/entrezdirect/esummary/tests/main.nf.test +++ b/modules/nf-core/entrezdirect/esummary/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test_sra' ], // meta map uid = '5135484', @@ -43,6 +44,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test_genome' ], // meta map uid = '768', @@ -71,6 +73,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test_assembly' ], // meta map uid = '191021', @@ -100,6 +103,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test_assembly' ], // meta map uid = '191021', diff --git a/modules/nf-core/epang/place/tests/main.nf.test b/modules/nf-core/epang/place/tests/main.nf.test index 78987c50efa..98604e97cf1 100644 --- a/modules/nf-core/epang/place/tests/main.nf.test +++ b/modules/nf-core/epang/place/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', model:'LG' ], // meta map file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/epang/query.alnfaa.gz', checkIfExists: true), @@ -49,6 +50,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', model:'LG' ], // meta map file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/epang/query.alnfaa.gz', checkIfExists: true), diff --git a/modules/nf-core/estsfs/tests/main.nf.test b/modules/nf-core/estsfs/tests/main.nf.test index 33e602d9d90..472ccc4e077 100644 --- a/modules/nf-core/estsfs/tests/main.nf.test +++ b/modules/nf-core/estsfs/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'delete_me/estsfs/config-JC.txt', checkIfExists: true), @@ -38,6 +39,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'delete_me/estsfs/config-JC.txt', checkIfExists: true), diff --git a/modules/nf-core/evigene/tr2aacds/tests/main.nf.test b/modules/nf-core/evigene/tr2aacds/tests/main.nf.test index 720550c9aea..04bfc79d251 100644 --- a/modules/nf-core/evigene/tr2aacds/tests/main.nf.test +++ b/modules/nf-core/evigene/tr2aacds/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map @@ -43,6 +44,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map diff --git a/modules/nf-core/expansionhunter/tests/main.nf.test b/modules/nf-core/expansionhunter/tests/main.nf.test index 40c0f2361e5..8b12b82deeb 100644 --- a/modules/nf-core/expansionhunter/tests/main.nf.test +++ b/modules/nf-core/expansionhunter/tests/main.nf.test @@ -12,6 +12,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), @@ -39,6 +40,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), diff --git a/modules/nf-core/expansionhunterdenovo/profile/tests/main.nf.test b/modules/nf-core/expansionhunterdenovo/profile/tests/main.nf.test index d77e9e248b2..ca080f57baa 100644 --- a/modules/nf-core/expansionhunterdenovo/profile/tests/main.nf.test +++ b/modules/nf-core/expansionhunterdenovo/profile/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), @@ -40,6 +41,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), diff --git a/modules/nf-core/falco/tests/main.nf.test b/modules/nf-core/falco/tests/main.nf.test index 816c72ba2a8..df19ba574cd 100644 --- a/modules/nf-core/falco/tests/main.nf.test +++ b/modules/nf-core/falco/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id: 'test', single_end:true ], [ @@ -44,6 +45,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id: 'test', single_end:false ], [ @@ -79,6 +81,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id: 'test', single_end:false ], [ diff --git a/modules/nf-core/famsa/align/tests/main.nf.test b/modules/nf-core/famsa/align/tests/main.nf.test index 8e91c3084e0..e8c947c0411 100644 --- a/modules/nf-core/famsa/align/tests/main.nf.test +++ b/modules/nf-core/famsa/align/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/contigs.fasta', checkIfExists: true) ] @@ -39,6 +40,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/contigs.fasta', checkIfExists: true) ] @@ -76,6 +78,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/contigs.fasta', checkIfExists: true) ] diff --git a/modules/nf-core/famsa/guidetree/tests/main.nf.test b/modules/nf-core/famsa/guidetree/tests/main.nf.test index 4c01a6e9c16..1647da43e09 100644 --- a/modules/nf-core/famsa/guidetree/tests/main.nf.test +++ b/modules/nf-core/famsa/guidetree/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/contigs.fasta', checkIfExists: true) ] diff --git a/modules/nf-core/faqcs/tests/main.nf.test b/modules/nf-core/faqcs/tests/main.nf.test index dc06e5c5eef..4f3a3b25a71 100644 --- a/modules/nf-core/faqcs/tests/main.nf.test +++ b/modules/nf-core/faqcs/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id: 'test', single_end:true ], [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ] @@ -41,6 +42,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [id: 'test', single_end: false], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), @@ -72,6 +74,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [id: 'test', single_end: false], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), @@ -103,6 +106,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id: 'test', single_end:true ], [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ] @@ -132,6 +136,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id: 'test', single_end:true ], [] ] """ } diff --git a/modules/nf-core/fargene/tests/main.nf.test b/modules/nf-core/fargene/tests/main.nf.test index 2f4e3fc6329..11f3660176d 100644 --- a/modules/nf-core/fargene/tests/main.nf.test +++ b/modules/nf-core/fargene/tests/main.nf.test @@ -29,6 +29,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = GUNZIP.out.gunzip input[1] = 'class_a' """ @@ -58,6 +59,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = GUNZIP.out.gunzip input[1] = 'class_a' """ diff --git a/modules/nf-core/fastani/tests/main.nf.test b/modules/nf-core/fastani/tests/main.nf.test index a4318db49ee..7bd080562bf 100644 --- a/modules/nf-core/fastani/tests/main.nf.test +++ b/modules/nf-core/fastani/tests/main.nf.test @@ -12,6 +12,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) diff --git a/modules/nf-core/fastavalidator/tests/main.nf.test b/modules/nf-core/fastavalidator/tests/main.nf.test index 39b00d8b968..2d52c644da8 100644 --- a/modules/nf-core/fastavalidator/tests/main.nf.test +++ b/modules/nf-core/fastavalidator/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) @@ -38,6 +39,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gff3', checkIfExists: true) diff --git a/modules/nf-core/fastawindows/tests/main.nf.test b/modules/nf-core/fastawindows/tests/main.nf.test index f4bea49f446..58bd5c0b468 100644 --- a/modules/nf-core/fastawindows/tests/main.nf.test +++ b/modules/nf-core/fastawindows/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) @@ -37,6 +38,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) diff --git a/modules/nf-core/fastk/fastk/tests/main.nf.test b/modules/nf-core/fastk/fastk/tests/main.nf.test index 856c36a8f8a..3267ea52853 100644 --- a/modules/nf-core/fastk/fastk/tests/main.nf.test +++ b/modules/nf-core/fastk/fastk/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' , single_end: true ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) @@ -36,6 +37,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' , single_end: false ], // meta map [ @@ -63,6 +65,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' , single_end: true ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) @@ -87,6 +90,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' , single_end: false ], // meta map [ diff --git a/modules/nf-core/fastme/tests/main.nf.test b/modules/nf-core/fastme/tests/main.nf.test index 3dcbf10714b..902c90c5b3e 100644 --- a/modules/nf-core/fastme/tests/main.nf.test +++ b/modules/nf-core/fastme/tests/main.nf.test @@ -30,6 +30,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = TCOFFEE_SEQREFORMAT.out.formatted_file .map { meta, aln -> [meta, aln, []] } """ @@ -75,6 +76,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = TCOFFEE_SEQREFORMAT.out.formatted_file .join(FAMSA_GUIDETREE.out.tree, by: 0) .map { meta, aln, tree -> [meta, aln, tree] } @@ -111,6 +113,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = TCOFFEE_SEQREFORMAT.out.formatted_file .map { meta, aln -> [meta, aln, []] } """ @@ -137,6 +140,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id: "test" ], file("https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/setoxin.ref", checkIfExists: true), [] diff --git a/modules/nf-core/fastp/tests/main.nf.test b/modules/nf-core/fastp/tests/main.nf.test index 30dbb8aabf2..a55f77d0632 100644 --- a/modules/nf-core/fastp/tests/main.nf.test +++ b/modules/nf-core/fastp/tests/main.nf.test @@ -85,6 +85,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:true ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz', checkIfExists: true) ] @@ -151,6 +152,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), @@ -184,6 +186,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), @@ -217,6 +220,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), @@ -250,6 +254,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:true ], [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ] @@ -285,6 +290,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), @@ -386,6 +392,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:true ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz', checkIfExists: true) ] @@ -442,6 +449,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), @@ -470,6 +478,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), @@ -498,6 +507,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), @@ -526,6 +536,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:true ], [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ] @@ -553,6 +564,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), diff --git a/modules/nf-core/fastqc/tests/main.nf.test b/modules/nf-core/fastqc/tests/main.nf.test index e9d79a074e8..ecd6f8bfe64 100644 --- a/modules/nf-core/fastqc/tests/main.nf.test +++ b/modules/nf-core/fastqc/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id: 'test', single_end:true ], [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ] @@ -40,6 +41,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [id: 'test', single_end: false], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), @@ -68,6 +70,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [id: 'test', single_end: false], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz', checkIfExists: true) @@ -92,6 +95,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [id: 'test', single_end: false], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) @@ -116,6 +120,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [id: 'test', single_end: false], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), @@ -152,6 +157,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'mysample', single_end:true ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) @@ -177,6 +183,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id: 'test', single_end:true ], [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ] @@ -199,6 +206,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [id: 'test', single_end: false], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), @@ -222,6 +230,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [id: 'test', single_end: false], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz', checkIfExists: true) @@ -244,6 +253,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [id: 'test', single_end: false], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) @@ -266,6 +276,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [id: 'test', single_end: false], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), @@ -291,6 +302,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'mysample', single_end:true ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) diff --git a/modules/nf-core/fastqscreen/buildfromindex/tests/main.nf.test b/modules/nf-core/fastqscreen/buildfromindex/tests/main.nf.test index 5357712af23..faa729829d9 100644 --- a/modules/nf-core/fastqscreen/buildfromindex/tests/main.nf.test +++ b/modules/nf-core/fastqscreen/buildfromindex/tests/main.nf.test @@ -31,6 +31,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = BOWTIE2_BUILD.out.index.map{meta, index -> meta.id}.collect() input[1] = BOWTIE2_BUILD.out.index.map{meta, index -> index}.collect() """ @@ -53,6 +54,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = BOWTIE2_BUILD.out.index.map{meta, index -> meta.id}.collect() input[1] = BOWTIE2_BUILD.out.index.map{meta, index -> index}.collect() """ diff --git a/modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test b/modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test index 71230a22404..d2926e8a393 100644 --- a/modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test +++ b/modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test @@ -43,6 +43,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [[ id:'test', single_end:true ], [file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ] ] @@ -68,6 +69,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [[ id:'test', single_end:false ], [file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)] ] @@ -97,6 +99,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [[ id:'test', single_end:true ], [file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ] ] diff --git a/modules/nf-core/fasttree/tests/main.nf.test b/modules/nf-core/fasttree/tests/main.nf.test index 1ae1ecae24c..48f8b01bade 100644 --- a/modules/nf-core/fasttree/tests/main.nf.test +++ b/modules/nf-core/fasttree/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/informative_sites.fas', checkIfExists: true) ] """ diff --git a/modules/nf-core/fastx/collapser/tests/main.nf.test b/modules/nf-core/fastx/collapser/tests/main.nf.test index b6f8bc3f3bc..3cabc6b259d 100644 --- a/modules/nf-core/fastx/collapser/tests/main.nf.test +++ b/modules/nf-core/fastx/collapser/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/fasta/alz.ccs.fasta', checkIfExists: true) @@ -41,6 +42,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/fasta/alz.ccs.fasta', checkIfExists: true) diff --git a/modules/nf-core/fcs/fcsadaptor/tests/main.nf.test b/modules/nf-core/fcs/fcsadaptor/tests/main.nf.test index 13caaceabb4..a958dadaf04 100644 --- a/modules/nf-core/fcs/fcsadaptor/tests/main.nf.test +++ b/modules/nf-core/fcs/fcsadaptor/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id: 'test' ], file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/genome/genome.fna.gz', checkIfExists: true) @@ -44,6 +45,7 @@ nextflow_process { when { process { """ + // testy mctestface def input_file_lines = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true).text.split('\\n') def file_with_adapters = file('sarscov2_with_adapters.fasta') file_with_adapters.text = ( @@ -87,6 +89,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id: 'test' ], file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/genome/genome.fna.gz', checkIfExists: true) diff --git a/modules/nf-core/ffq/tests/main.nf.test b/modules/nf-core/ffq/tests/main.nf.test index 680a4f3b0b4..b28fefdcf79 100644 --- a/modules/nf-core/ffq/tests/main.nf.test +++ b/modules/nf-core/ffq/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ 'SRR9990627' ] """ @@ -33,6 +34,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ 'SRR9990627', 'SRX7347523' ] """ diff --git a/modules/nf-core/fgbio/callduplexconsensusreads/tests/main.nf.test b/modules/nf-core/fgbio/callduplexconsensusreads/tests/main.nf.test index 0144e0ea5e6..d9387e80577 100644 --- a/modules/nf-core/fgbio/callduplexconsensusreads/tests/main.nf.test +++ b/modules/nf-core/fgbio/callduplexconsensusreads/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/umi/test.paired_end.duplex_umi_grouped.bam', checkIfExists: true) @@ -40,6 +41,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/umi/test.paired_end.duplex_umi_grouped.bam', checkIfExists: true) diff --git a/modules/nf-core/fgbio/callmolecularconsensusreads/tests/main.nf.test b/modules/nf-core/fgbio/callmolecularconsensusreads/tests/main.nf.test index 8a906340518..b00d4b98d3c 100644 --- a/modules/nf-core/fgbio/callmolecularconsensusreads/tests/main.nf.test +++ b/modules/nf-core/fgbio/callmolecularconsensusreads/tests/main.nf.test @@ -30,6 +30,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = FGBIO_SORTBAM.out.bam input[1] = 1 input[2] = 20 @@ -53,6 +54,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = FGBIO_SORTBAM.out.bam input[1] = 1 input[2] = 20 diff --git a/modules/nf-core/fgbio/collectduplexseqmetrics/tests/main.nf.test b/modules/nf-core/fgbio/collectduplexseqmetrics/tests/main.nf.test index 0021229b1ba..343e636035a 100644 --- a/modules/nf-core/fgbio/collectduplexseqmetrics/tests/main.nf.test +++ b/modules/nf-core/fgbio/collectduplexseqmetrics/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.duplex_umi_grouped.bam', checkIfExists: true) @@ -49,6 +50,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.duplex_umi_grouped.bam', checkIfExists: true) diff --git a/modules/nf-core/fgbio/fastqtobam/tests/main.nf.test b/modules/nf-core/fgbio/fastqtobam/tests/main.nf.test index d10a005220f..b59b1b9ae39 100644 --- a/modules/nf-core/fgbio/fastqtobam/tests/main.nf.test +++ b/modules/nf-core/fgbio/fastqtobam/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ @@ -44,6 +45,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ @@ -74,6 +76,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ @@ -103,6 +106,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ @@ -132,6 +136,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ @@ -162,6 +167,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ @@ -192,6 +198,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ diff --git a/modules/nf-core/fgbio/filterconsensusreads/tests/main.nf.test b/modules/nf-core/fgbio/filterconsensusreads/tests/main.nf.test index e4f3511ffec..2385835747f 100644 --- a/modules/nf-core/fgbio/filterconsensusreads/tests/main.nf.test +++ b/modules/nf-core/fgbio/filterconsensusreads/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [[ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/umi/test.paired_end.duplex_umi_duplex_consensus.bam', checkIfExists: true) ] @@ -44,6 +45,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [[ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/umi/test.paired_end.duplex_umi_duplex_consensus.bam', checkIfExists: true) ] diff --git a/modules/nf-core/fgbio/groupreadsbyumi/tests/main.nf.test b/modules/nf-core/fgbio/groupreadsbyumi/tests/main.nf.test index a9e8bd256c0..47a70d64ded 100644 --- a/modules/nf-core/fgbio/groupreadsbyumi/tests/main.nf.test +++ b/modules/nf-core/fgbio/groupreadsbyumi/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/umi/test.paired_end.unsorted_tagged.bam', checkIfExists: true) @@ -39,6 +40,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/umi/test.paired_end.unsorted_tagged.bam', checkIfExists: true) diff --git a/modules/nf-core/fgbio/sortbam/tests/main.nf.test b/modules/nf-core/fgbio/sortbam/tests/main.nf.test index 2e9b2459679..21b11d4cad8 100644 --- a/modules/nf-core/fgbio/sortbam/tests/main.nf.test +++ b/modules/nf-core/fgbio/sortbam/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) ] @@ -37,6 +38,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) ] diff --git a/modules/nf-core/fgbio/zipperbams/tests/main.nf.test b/modules/nf-core/fgbio/zipperbams/tests/main.nf.test index 89f7ce5cfb5..ea09cac3809 100644 --- a/modules/nf-core/fgbio/zipperbams/tests/main.nf.test +++ b/modules/nf-core/fgbio/zipperbams/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/umi/test.paired_end.duplex_umi_unmapped.bam', checkIfExists: true) @@ -51,6 +52,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/umi/test.paired_end.duplex_umi_unmapped.bam', checkIfExists: true) diff --git a/modules/nf-core/flye/tests/main.nf.test b/modules/nf-core/flye/tests/main.nf.test index afbf926ef49..6ccc7592e37 100644 --- a/modules/nf-core/flye/tests/main.nf.test +++ b/modules/nf-core/flye/tests/main.nf.test @@ -154,6 +154,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/fastq/test_hifi.fastq.gz', checkIfExists: true) ] diff --git a/modules/nf-core/foldcomp/compress/tests/main.nf.test b/modules/nf-core/foldcomp/compress/tests/main.nf.test index 0c0bd14bd35..f6074f60e4a 100644 --- a/modules/nf-core/foldcomp/compress/tests/main.nf.test +++ b/modules/nf-core/foldcomp/compress/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'proteomics/pdb/1tim.pdb', checkIfExists: true) @@ -85,6 +86,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'proteomics/pdb/1tim.pdb', checkIfExists: true) diff --git a/modules/nf-core/foldcomp/decompress/tests/main.nf.test b/modules/nf-core/foldcomp/decompress/tests/main.nf.test index a8f40acdf2e..ea82eb13442 100644 --- a/modules/nf-core/foldcomp/decompress/tests/main.nf.test +++ b/modules/nf-core/foldcomp/decompress/tests/main.nf.test @@ -29,6 +29,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = FOLDCOMP_COMPRESS.out.fcz.flatMap { meta, files -> files.collect { file -> tuple(meta, file) } } @@ -52,6 +53,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = FOLDCOMP_COMPRESS.out.fcz """ } diff --git a/modules/nf-core/foldseek/createdb/tests/main.nf.test b/modules/nf-core/foldseek/createdb/tests/main.nf.test index 03064df16ba..39d6a74ea27 100644 --- a/modules/nf-core/foldseek/createdb/tests/main.nf.test +++ b/modules/nf-core/foldseek/createdb/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id:'test'], file(params.modules_testdata_base_path + 'proteomics/pdb/1tim.pdb', checkIfExists: true) ] """ } @@ -34,6 +35,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id:'test'], file(params.modules_testdata_base_path + 'proteomics/pdb/1tim.pdb', checkIfExists: true) ] """ } diff --git a/modules/nf-core/foldseek/easysearch/tests/main.nf.test b/modules/nf-core/foldseek/easysearch/tests/main.nf.test index c71e2743ed1..899392f9f2d 100644 --- a/modules/nf-core/foldseek/easysearch/tests/main.nf.test +++ b/modules/nf-core/foldseek/easysearch/tests/main.nf.test @@ -25,6 +25,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test_search' ], [ file(params.modules_testdata_base_path + 'proteomics/pdb/8tim.pdb', checkIfExists: true) ] ] input[1] = FOLDSEEK_CREATEDB.out.db """ @@ -48,6 +49,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test_search' ], [ file(params.modules_testdata_base_path + 'proteomics/pdb/8tim.pdb', checkIfExists: true) ] ] input[1] = FOLDSEEK_CREATEDB.out.db """ diff --git a/modules/nf-core/fq/generate/tests/main.nf.test b/modules/nf-core/fq/generate/tests/main.nf.test index 9029120333a..e434938d093 100644 --- a/modules/nf-core/fq/generate/tests/main.nf.test +++ b/modules/nf-core/fq/generate/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of( [ id:'test', single_end:false ] ) """ } @@ -33,6 +34,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of( [ id:'test', single_end:false ] ) """ } diff --git a/modules/nf-core/freebayes/tests/main.nf.test b/modules/nf-core/freebayes/tests/main.nf.test index eb2d7a8055d..507a100ea9d 100644 --- a/modules/nf-core/freebayes/tests/main.nf.test +++ b/modules/nf-core/freebayes/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), @@ -49,6 +50,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), @@ -85,6 +87,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), @@ -121,6 +124,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), @@ -157,6 +161,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), diff --git a/modules/nf-core/freyja/boot/tests/main.nf.test b/modules/nf-core/freyja/boot/tests/main.nf.test index 831fd1507df..5f0fb8893eb 100644 --- a/modules/nf-core/freyja/boot/tests/main.nf.test +++ b/modules/nf-core/freyja/boot/tests/main.nf.test @@ -40,6 +40,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = FREYJA_VARIANTS.out.variants input[1] = 3 input[2] = FREYJA_UPDATE.out.barcodes diff --git a/modules/nf-core/freyja/demix/tests/main.nf.test b/modules/nf-core/freyja/demix/tests/main.nf.test index bd300e9c71b..08f5029babc 100644 --- a/modules/nf-core/freyja/demix/tests/main.nf.test +++ b/modules/nf-core/freyja/demix/tests/main.nf.test @@ -40,6 +40,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = FREYJA_VARIANTS.out.variants input[1] = FREYJA_UPDATE.out.barcodes input[2] = FREYJA_UPDATE.out.lineages_meta diff --git a/modules/nf-core/freyja/update/tests/main.nf.test b/modules/nf-core/freyja/update/tests/main.nf.test index e1c293ccceb..f208b6fe0c7 100644 --- a/modules/nf-core/freyja/update/tests/main.nf.test +++ b/modules/nf-core/freyja/update/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = "test_db" """ } diff --git a/modules/nf-core/freyja/variants/tests/main.nf.test b/modules/nf-core/freyja/variants/tests/main.nf.test index aca4db1695f..3659ae82e47 100644 --- a/modules/nf-core/freyja/variants/tests/main.nf.test +++ b/modules/nf-core/freyja/variants/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) diff --git a/modules/nf-core/gamma/gamma/tests/main.nf.test b/modules/nf-core/gamma/gamma/tests/main.nf.test index 6f7536ba47b..d5b8bce0d16 100644 --- a/modules/nf-core/gamma/gamma/tests/main.nf.test +++ b/modules/nf-core/gamma/gamma/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/fasta/test1.contigs.fa.gz', checkIfExists: true) @@ -39,6 +40,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) diff --git a/modules/nf-core/ganon/buildcustom/tests/main.nf.test b/modules/nf-core/ganon/buildcustom/tests/main.nf.test index 3d97408bbdb..67341b058cf 100644 --- a/modules/nf-core/ganon/buildcustom/tests/main.nf.test +++ b/modules/nf-core/ganon/buildcustom/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true), @@ -43,6 +44,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true), diff --git a/modules/nf-core/ganon/classify/tests/main.nf.test b/modules/nf-core/ganon/classify/tests/main.nf.test index e581ca065eb..13b6160ab9a 100644 --- a/modules/nf-core/ganon/classify/tests/main.nf.test +++ b/modules/nf-core/ganon/classify/tests/main.nf.test @@ -32,6 +32,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map [ @@ -59,6 +60,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ @@ -89,6 +91,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map [ diff --git a/modules/nf-core/ganon/report/tests/main.nf.test b/modules/nf-core/ganon/report/tests/main.nf.test index d350eed066b..99ea7c02ae5 100644 --- a/modules/nf-core/ganon/report/tests/main.nf.test +++ b/modules/nf-core/ganon/report/tests/main.nf.test @@ -47,6 +47,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = GANON_CLASSIFY.out.report input[1] = GANON_BUILDCUSTOM.out.db.map{it[1]} """ @@ -69,6 +70,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = GANON_CLASSIFY.out.report input[1] = GANON_BUILDCUSTOM.out.db.map{it[1]} """ diff --git a/modules/nf-core/ganon/table/tests/main.nf.test b/modules/nf-core/ganon/table/tests/main.nf.test index 43b6cf0a1d1..b2a53709180 100644 --- a/modules/nf-core/ganon/table/tests/main.nf.test +++ b/modules/nf-core/ganon/table/tests/main.nf.test @@ -57,6 +57,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = GANON_REPORT.out.tre.collect{it[1]}.map{[[id: "db1"], it]} """ } @@ -78,6 +79,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = GANON_REPORT.out.tre.collect{it[1]}.map{[[id: "db1"], it]} """ } diff --git a/modules/nf-core/gappa/examineassign/tests/main.nf.test b/modules/nf-core/gappa/examineassign/tests/main.nf.test index f138fef34e5..53f5b47b4ee 100644 --- a/modules/nf-core/gappa/examineassign/tests/main.nf.test +++ b/modules/nf-core/gappa/examineassign/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/gappa/epa_result.jplace.gz', checkIfExists: true), @@ -49,6 +50,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/gappa/epa_result.jplace.gz', checkIfExists: true), diff --git a/modules/nf-core/gappa/examinegraft/tests/main.nf.test b/modules/nf-core/gappa/examinegraft/tests/main.nf.test index 220ab495712..e03855240fd 100644 --- a/modules/nf-core/gappa/examinegraft/tests/main.nf.test +++ b/modules/nf-core/gappa/examinegraft/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/gappa/epa_result.jplace.gz', checkIfExists: true) @@ -38,6 +39,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/gappa/epa_result.jplace.gz', checkIfExists: true) diff --git a/modules/nf-core/gappa/examineheattree/tests/main.nf.test b/modules/nf-core/gappa/examineheattree/tests/main.nf.test index fbb2758d03d..7e1a603efe1 100644 --- a/modules/nf-core/gappa/examineheattree/tests/main.nf.test +++ b/modules/nf-core/gappa/examineheattree/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/gappa/epa_result.jplace.gz', checkIfExists: true) @@ -48,6 +49,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/gappa/epa_result.jplace.gz', checkIfExists: true) diff --git a/modules/nf-core/gatk/realignertargetcreator/tests/main.nf.test b/modules/nf-core/gatk/realignertargetcreator/tests/main.nf.test index 1b1098d00a2..9a57be68eab 100644 --- a/modules/nf-core/gatk/realignertargetcreator/tests/main.nf.test +++ b/modules/nf-core/gatk/realignertargetcreator/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), diff --git a/modules/nf-core/gatk/unifiedgenotyper/tests/main.nf.test b/modules/nf-core/gatk/unifiedgenotyper/tests/main.nf.test index 8d22aabdcfc..0114e39574d 100644 --- a/modules/nf-core/gatk/unifiedgenotyper/tests/main.nf.test +++ b/modules/nf-core/gatk/unifiedgenotyper/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), diff --git a/modules/nf-core/gatk4/addorreplacereadgroups/tests/main.nf.test b/modules/nf-core/gatk4/addorreplacereadgroups/tests/main.nf.test index cd140e82776..7a75c2adc70 100644 --- a/modules/nf-core/gatk4/addorreplacereadgroups/tests/main.nf.test +++ b/modules/nf-core/gatk4/addorreplacereadgroups/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [:], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) ] input[1] = [ [:], [] ] input[2] = [ [:], [] ] @@ -38,6 +39,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ @@ -66,6 +68,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [:], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) ] input[1] = [ [:], [] ] input[2] = [ [:], [] ] diff --git a/modules/nf-core/gatk4/annotateintervals/tests/main.nf.test b/modules/nf-core/gatk4/annotateintervals/tests/main.nf.test index 0f81e1ea606..8ec2c313fc5 100644 --- a/modules/nf-core/gatk4/annotateintervals/tests/main.nf.test +++ b/modules/nf-core/gatk4/annotateintervals/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true) @@ -43,6 +44,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ @@ -74,6 +76,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.interval_list', checkIfExists: true) @@ -102,6 +105,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.interval_list', checkIfExists: true) @@ -130,6 +134,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.interval_list', checkIfExists: true) @@ -160,6 +165,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true) diff --git a/modules/nf-core/gatk4/applybqsr/tests/main.nf.test b/modules/nf-core/gatk4/applybqsr/tests/main.nf.test index acb41ce1e47..008dc19503a 100644 --- a/modules/nf-core/gatk4/applybqsr/tests/main.nf.test +++ b/modules/nf-core/gatk4/applybqsr/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), @@ -42,6 +43,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), @@ -69,6 +71,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), @@ -99,6 +102,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), @@ -128,6 +132,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), diff --git a/modules/nf-core/gatk4/applyvqsr/tests/main.nf.test b/modules/nf-core/gatk4/applyvqsr/tests/main.nf.test index 104eb7f01b4..67733ff7dc6 100644 --- a/modules/nf-core/gatk4/applyvqsr/tests/main.nf.test +++ b/modules/nf-core/gatk4/applyvqsr/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi', checkIfExists: true), @@ -48,6 +49,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi', checkIfExists: true), @@ -80,6 +82,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi', checkIfExists: true), diff --git a/modules/nf-core/gatk4/asereadcounter/main.nf.test b/modules/nf-core/gatk4/asereadcounter/main.nf.test index 9f80708f01e..00cc7b6f319 100644 --- a/modules/nf-core/gatk4/asereadcounter/main.nf.test +++ b/modules/nf-core/gatk4/asereadcounter/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path +'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), diff --git a/modules/nf-core/gatk4/baserecalibrator/tests/main.nf.test b/modules/nf-core/gatk4/baserecalibrator/tests/main.nf.test index fbd91beae2b..d69d5f94d11 100644 --- a/modules/nf-core/gatk4/baserecalibrator/tests/main.nf.test +++ b/modules/nf-core/gatk4/baserecalibrator/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), @@ -42,6 +43,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map @@ -72,6 +74,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map @@ -110,6 +113,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [], @@ -139,6 +143,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), diff --git a/modules/nf-core/gatk4/bedtointervallist/tests/main.nf.test b/modules/nf-core/gatk4/bedtointervallist/tests/main.nf.test index 2289f73fa42..8b07989bd66 100644 --- a/modules/nf-core/gatk4/bedtointervallist/tests/main.nf.test +++ b/modules/nf-core/gatk4/bedtointervallist/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) ] diff --git a/modules/nf-core/gatk4/calculatecontamination/tests/main.nf.test b/modules/nf-core/gatk4/calculatecontamination/tests/main.nf.test index 81f048f67b8..b7d73e835b2 100644 --- a/modules/nf-core/gatk4/calculatecontamination/tests/main.nf.test +++ b/modules/nf-core/gatk4/calculatecontamination/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/test2.pileups.table', checkIfExists: true), [] ] @@ -36,6 +37,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/test2.pileups.table', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/test.pileups.table', checkIfExists: true) @@ -61,6 +63,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/test2.pileups.table', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/test.pileups.table', checkIfExists: true) @@ -87,6 +90,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/test2.pileups.table', checkIfExists: true), [] ] diff --git a/modules/nf-core/gatk4/calibratedragstrmodel/tests/main.nf.test b/modules/nf-core/gatk4/calibratedragstrmodel/tests/main.nf.test index f06292f2eed..79e9090d086 100644 --- a/modules/nf-core/gatk4/calibratedragstrmodel/tests/main.nf.test +++ b/modules/nf-core/gatk4/calibratedragstrmodel/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), @@ -46,6 +47,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), @@ -77,6 +79,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), @@ -108,6 +111,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), diff --git a/modules/nf-core/gatk4/collectreadcounts/tests/main.nf.test b/modules/nf-core/gatk4/collectreadcounts/tests/main.nf.test index 0832cf85a24..a680cc7ac74 100644 --- a/modules/nf-core/gatk4/collectreadcounts/tests/main.nf.test +++ b/modules/nf-core/gatk4/collectreadcounts/tests/main.nf.test @@ -17,6 +17,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), @@ -50,6 +51,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), @@ -79,6 +81,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), diff --git a/modules/nf-core/gatk4/collectsvevidence/tests/main.nf.test b/modules/nf-core/gatk4/collectsvevidence/tests/main.nf.test index 418554bb345..bd7f9896fc8 100644 --- a/modules/nf-core/gatk4/collectsvevidence/tests/main.nf.test +++ b/modules/nf-core/gatk4/collectsvevidence/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), @@ -51,6 +52,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), @@ -86,6 +88,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), @@ -125,6 +128,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), @@ -155,6 +159,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), diff --git a/modules/nf-core/gatk4/combinegvcfs/tests/main.nf.test b/modules/nf-core/gatk4/combinegvcfs/tests/main.nf.test index df2d5b4e5ef..549b69e3451 100644 --- a/modules/nf-core/gatk4/combinegvcfs/tests/main.nf.test +++ b/modules/nf-core/gatk4/combinegvcfs/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf', checkIfExists: true), @@ -43,6 +44,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf', checkIfExists: true), diff --git a/modules/nf-core/gatk4/composestrtablefile/tests/main.nf.test b/modules/nf-core/gatk4/composestrtablefile/tests/main.nf.test index 7d066cf1ffb..cf888939749 100644 --- a/modules/nf-core/gatk4/composestrtablefile/tests/main.nf.test +++ b/modules/nf-core/gatk4/composestrtablefile/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) diff --git a/modules/nf-core/gatk4/condensedepthevidence/tests/main.nf.test b/modules/nf-core/gatk4/condensedepthevidence/tests/main.nf.test index e681d0bddaa..64e94016d23 100644 --- a/modules/nf-core/gatk4/condensedepthevidence/tests/main.nf.test +++ b/modules/nf-core/gatk4/condensedepthevidence/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/condensedepthevidence/testN.rd.txt.gz", checkIfExists: true), @@ -48,6 +49,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/condensedepthevidence/testN.rd.txt.gz", checkIfExists: true), diff --git a/modules/nf-core/gatk4/createsequencedictionary/tests/main.nf.test b/modules/nf-core/gatk4/createsequencedictionary/tests/main.nf.test index a8a9c6d2e86..dd644c1db95 100644 --- a/modules/nf-core/gatk4/createsequencedictionary/tests/main.nf.test +++ b/modules/nf-core/gatk4/createsequencedictionary/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] @@ -37,6 +38,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] diff --git a/modules/nf-core/gatk4/denoisereadcounts/tests/main.nf.test b/modules/nf-core/gatk4/denoisereadcounts/tests/main.nf.test index e5fef2a2a24..f255ff53a48 100644 --- a/modules/nf-core/gatk4/denoisereadcounts/tests/main.nf.test +++ b/modules/nf-core/gatk4/denoisereadcounts/tests/main.nf.test @@ -55,6 +55,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = GATK4_COLLECTREADCOUNTS.out.tsv.first() input[1] = GATK4_CREATEREADCOUNTPANELOFNORMALS.out.pon """ diff --git a/modules/nf-core/gatk4/estimatelibrarycomplexity/tests/main.nf.test b/modules/nf-core/gatk4/estimatelibrarycomplexity/tests/main.nf.test index e23b65573c9..849d8e27433 100644 --- a/modules/nf-core/gatk4/estimatelibrarycomplexity/tests/main.nf.test +++ b/modules/nf-core/gatk4/estimatelibrarycomplexity/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface // [ meta, input ] input[0] = [ [ id:'test', single_end:false ], // meta map @@ -47,6 +48,7 @@ nextflow_process { when { process { """ + // testy mctestface // [ meta, input ] input[0] = [ [ id:'test', single_end:false ], // meta map @@ -82,6 +84,7 @@ nextflow_process { when { process { """ + // testy mctestface // [ meta, input ] input[0] = [ [ id:'test', single_end:false ], // meta map diff --git a/modules/nf-core/gatk4/fastqtosam/tests/main.nf.test b/modules/nf-core/gatk4/fastqtosam/tests/main.nf.test index 8ba0ff044c5..a33a68401cc 100644 --- a/modules/nf-core/gatk4/fastqtosam/tests/main.nf.test +++ b/modules/nf-core/gatk4/fastqtosam/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ] @@ -40,6 +41,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) @@ -67,6 +69,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ] diff --git a/modules/nf-core/gatk4/filterintervals/tests/main.nf.test b/modules/nf-core/gatk4/filterintervals/tests/main.nf.test index a84f562e394..bea3af5e1dd 100644 --- a/modules/nf-core/gatk4/filterintervals/tests/main.nf.test +++ b/modules/nf-core/gatk4/filterintervals/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.preprocessed_intervals.interval_list', checkIfExists: true) diff --git a/modules/nf-core/gatk4/filtermutectcalls/tests/main.nf.test b/modules/nf-core/gatk4/filtermutectcalls/tests/main.nf.test index 83c3703fcbc..740dde97cda 100644 --- a/modules/nf-core/gatk4/filtermutectcalls/tests/main.nf.test +++ b/modules/nf-core/gatk4/filtermutectcalls/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz', checkIfExists: true), @@ -56,6 +57,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz', checkIfExists: true), @@ -97,6 +99,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz', checkIfExists: true), @@ -140,6 +143,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz', checkIfExists: true), diff --git a/modules/nf-core/gatk4/gatherbqsrreports/tests/main.nf.test b/modules/nf-core/gatk4/gatherbqsrreports/tests/main.nf.test index 173b149b547..0e105d01860 100644 --- a/modules/nf-core/gatk4/gatherbqsrreports/tests/main.nf.test +++ b/modules/nf-core/gatk4/gatherbqsrreports/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/test.baserecalibrator.table', checkIfExists: true) @@ -37,6 +38,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ diff --git a/modules/nf-core/gatk4/gatherpileupsummaries/tests/main.nf.test b/modules/nf-core/gatk4/gatherpileupsummaries/tests/main.nf.test index f33c6a0d948..68cf195a4b6 100644 --- a/modules/nf-core/gatk4/gatherpileupsummaries/tests/main.nf.test +++ b/modules/nf-core/gatk4/gatherpileupsummaries/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/test.pileups.table', checkIfExists: true) ] @@ -41,6 +42,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/test.pileups.table', checkIfExists: true) ] diff --git a/modules/nf-core/gatk4/genomicsdbimport/tests/main.nf.test b/modules/nf-core/gatk4/genomicsdbimport/tests/main.nf.test index 5fef5dd2544..93267972c40 100644 --- a/modules/nf-core/gatk4/genomicsdbimport/tests/main.nf.test +++ b/modules/nf-core/gatk4/genomicsdbimport/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface // [meta, vcf, tbi, interval, interval_value, workspace ] input[0] = [ [ id:'test'], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true) , @@ -62,6 +63,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [id:"test"], [], [], [], []]).combine(UNTAR.out.untar.map{ it[1] }) // run_intlist input[1] = true @@ -102,6 +104,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [id:"test"], file( params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.gz' , checkIfExists: true), file( params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.gz.tbi' , checkIfExists: true), [], []]).combine(UNTAR.out.untar.map{ it[1] }) // run_intlist input[1] = false @@ -133,6 +136,7 @@ nextflow_process { when { process { """ + // testy mctestface // [meta, vcf, tbi, interval, interval_value, workspace ] input[0] = [ [ id:'test'], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true) , diff --git a/modules/nf-core/gatk4/genotypegvcfs/tests/main.nf.test b/modules/nf-core/gatk4/genotypegvcfs/tests/main.nf.test index 25bc2d3806b..aa71340d4e3 100644 --- a/modules/nf-core/gatk4/genotypegvcfs/tests/main.nf.test +++ b/modules/nf-core/gatk4/genotypegvcfs/tests/main.nf.test @@ -29,6 +29,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id:"test"], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf', checkIfExists: true), @@ -72,6 +73,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id:"test"], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true), @@ -121,6 +123,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id:"test"], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true), @@ -164,6 +167,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = UNTAR.out.untar.map { meta, gendb -> [ meta, gendb, [], [], []] } input[1] = [ [id:"fasta"], @@ -201,6 +205,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = UNTAR.out.untar.map { meta, gendb -> [ meta, @@ -248,6 +253,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id:"test"], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf', checkIfExists: true), diff --git a/modules/nf-core/gatk4/getpileupsummaries/tests/main.nf.test b/modules/nf-core/gatk4/getpileupsummaries/tests/main.nf.test index 79cd6344cb5..5de064ffb9d 100644 --- a/modules/nf-core/gatk4/getpileupsummaries/tests/main.nf.test +++ b/modules/nf-core/gatk4/getpileupsummaries/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam', checkIfExists: true) , file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam.bai', checkIfExists: true), @@ -42,6 +43,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram', checkIfExists: true) , file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram.crai', checkIfExists: true), @@ -78,6 +80,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam', checkIfExists: true) , file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam.bai', checkIfExists: true), diff --git a/modules/nf-core/gatk4/haplotypecaller/tests/main.nf.test b/modules/nf-core/gatk4/haplotypecaller/tests/main.nf.test index 18d35f498c6..7bbe5ed7679 100644 --- a/modules/nf-core/gatk4/haplotypecaller/tests/main.nf.test +++ b/modules/nf-core/gatk4/haplotypecaller/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test_bam' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), @@ -51,6 +52,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test_cram' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), @@ -86,6 +88,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test_cram_sites' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), @@ -121,6 +124,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test_cram_sites_dragstr' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), diff --git a/modules/nf-core/gatk4/indexfeaturefile/tests/main.nf.test b/modules/nf-core/gatk4/indexfeaturefile/tests/main.nf.test index 994606f1469..9abb5e009d1 100644 --- a/modules/nf-core/gatk4/indexfeaturefile/tests/main.nf.test +++ b/modules/nf-core/gatk4/indexfeaturefile/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true) @@ -38,6 +39,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed.gz', checkIfExists: true) @@ -61,6 +63,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf', checkIfExists: true) @@ -84,6 +87,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true) diff --git a/modules/nf-core/gatk4/intervallisttools/tests/main.nf.test b/modules/nf-core/gatk4/intervallisttools/tests/main.nf.test index 2891bf9e4b1..af7ed7ce125 100644 --- a/modules/nf-core/gatk4/intervallisttools/tests/main.nf.test +++ b/modules/nf-core/gatk4/intervallisttools/tests/main.nf.test @@ -34,6 +34,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = GATK4_BEDTOINTERVALLIST.out.interval_list """ } @@ -55,6 +56,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = GATK4_BEDTOINTERVALLIST.out.interval_list """ } diff --git a/modules/nf-core/gatk4/learnreadorientationmodel/tests/main.nf.test b/modules/nf-core/gatk4/learnreadorientationmodel/tests/main.nf.test index bffe02e4f6c..7a872e83529 100644 --- a/modules/nf-core/gatk4/learnreadorientationmodel/tests/main.nf.test +++ b/modules/nf-core/gatk4/learnreadorientationmodel/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.f1r2.tar.gz', checkIfExists: true)] ] diff --git a/modules/nf-core/gatk4/leftalignandtrimvariants/tests/main.nf.test b/modules/nf-core/gatk4/leftalignandtrimvariants/tests/main.nf.test index 581d730e5ac..9ff8d141481 100644 --- a/modules/nf-core/gatk4/leftalignandtrimvariants/tests/main.nf.test +++ b/modules/nf-core/gatk4/leftalignandtrimvariants/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true), @@ -47,6 +48,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true), diff --git a/modules/nf-core/gatk4/markduplicates/tests/main.nf.test b/modules/nf-core/gatk4/markduplicates/tests/main.nf.test index bbcf74db674..3b11f405a12 100644 --- a/modules/nf-core/gatk4/markduplicates/tests/main.nf.test +++ b/modules/nf-core/gatk4/markduplicates/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) @@ -42,6 +43,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], [ @@ -73,6 +75,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ @@ -105,6 +108,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], [] diff --git a/modules/nf-core/gatk4/mergebamalignment/tests/main.nf.test b/modules/nf-core/gatk4/mergebamalignment/tests/main.nf.test index 96e93bb1995..129ce102ec6 100644 --- a/modules/nf-core/gatk4/mergebamalignment/tests/main.nf.test +++ b/modules/nf-core/gatk4/mergebamalignment/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.bam', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.unaligned.bam', checkIfExists: true) @@ -47,6 +48,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.bam', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.unaligned.bam', checkIfExists: true) diff --git a/modules/nf-core/gatk4/mergemutectstats/tests/main.nf.test b/modules/nf-core/gatk4/mergemutectstats/tests/main.nf.test index 5f5ab40233b..55b09c33c24 100644 --- a/modules/nf-core/gatk4/mergemutectstats/tests/main.nf.test +++ b/modules/nf-core/gatk4/mergemutectstats/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz.stats', checkIfExists: true) ] @@ -38,6 +39,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz.stats', checkIfExists: true) ] diff --git a/modules/nf-core/gatk4/mergevcfs/tests/main.nf.test b/modules/nf-core/gatk4/mergevcfs/tests/main.nf.test index 77ace10a21b..d4321e45e86 100644 --- a/modules/nf-core/gatk4/mergevcfs/tests/main.nf.test +++ b/modules/nf-core/gatk4/mergevcfs/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz', checkIfExists: true) ]] input[1] = [ [], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true)] """ @@ -37,6 +38,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz', checkIfExists: true) ]] input[1] = [ [],[]] """ @@ -64,6 +66,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz', checkIfExists: true) ]] input[1] = [ [],[]] """ diff --git a/modules/nf-core/gatk4/preprocessintervals/tests/main.nf.test b/modules/nf-core/gatk4/preprocessintervals/tests/main.nf.test index a546fac5aa3..d5bb7219155 100644 --- a/modules/nf-core/gatk4/preprocessintervals/tests/main.nf.test +++ b/modules/nf-core/gatk4/preprocessintervals/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) diff --git a/modules/nf-core/gatk4/printreads/tests/main.nf.test b/modules/nf-core/gatk4/printreads/tests/main.nf.test index c0788619700..fab96662a27 100644 --- a/modules/nf-core/gatk4/printreads/tests/main.nf.test +++ b/modules/nf-core/gatk4/printreads/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), @@ -56,6 +57,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), diff --git a/modules/nf-core/gatk4/reblockgvcf/tests/main.nf.test b/modules/nf-core/gatk4/reblockgvcf/tests/main.nf.test index 55c65bbb22c..537bbb7f054 100644 --- a/modules/nf-core/gatk4/reblockgvcf/tests/main.nf.test +++ b/modules/nf-core/gatk4/reblockgvcf/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [[ id:'test', single_end:false ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi', checkIfExists: true), []] input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) @@ -41,6 +42,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [[ id:'test', single_end:false ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true)] input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) @@ -72,6 +74,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [[ id:'test', single_end:false ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi', checkIfExists: true), []] input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) diff --git a/modules/nf-core/gatk4/revertsam/tests/main.nf.test b/modules/nf-core/gatk4/revertsam/tests/main.nf.test index b5268048587..161ccedc2bd 100644 --- a/modules/nf-core/gatk4/revertsam/tests/main.nf.test +++ b/modules/nf-core/gatk4/revertsam/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) ] @@ -40,6 +41,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) ] diff --git a/modules/nf-core/gatk4/samtofastq/tests/main.nf.test b/modules/nf-core/gatk4/samtofastq/tests/main.nf.test index 30a41adddf6..a907cac70c0 100644 --- a/modules/nf-core/gatk4/samtofastq/tests/main.nf.test +++ b/modules/nf-core/gatk4/samtofastq/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end: true ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.bam', checkIfExists: true) ] ] @@ -40,6 +41,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end: false ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) ] ] @@ -65,6 +67,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end: true ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.bam', checkIfExists: true) ] ] diff --git a/modules/nf-core/gatk4/selectvariants/tests/main.nf.test b/modules/nf-core/gatk4/selectvariants/tests/main.nf.test index d8a97d2c53a..97eb4eb472d 100644 --- a/modules/nf-core/gatk4/selectvariants/tests/main.nf.test +++ b/modules/nf-core/gatk4/selectvariants/tests/main.nf.test @@ -42,6 +42,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true), diff --git a/modules/nf-core/gatk4/shiftfasta/tests/main.nf.test b/modules/nf-core/gatk4/shiftfasta/tests/main.nf.test index d11d144ea6e..4b90bcc1e6e 100644 --- a/modules/nf-core/gatk4/shiftfasta/tests/main.nf.test +++ b/modules/nf-core/gatk4/shiftfasta/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) diff --git a/modules/nf-core/gatk4/splitcram/tests/main.nf.test b/modules/nf-core/gatk4/splitcram/tests/main.nf.test index 18417f0ff4f..a0d97920605 100644 --- a/modules/nf-core/gatk4/splitcram/tests/main.nf.test +++ b/modules/nf-core/gatk4/splitcram/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true) @@ -43,6 +44,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true) diff --git a/modules/nf-core/gatk4/splitintervals/tests/main.nf.test b/modules/nf-core/gatk4/splitintervals/tests/main.nf.test index 26c20f88f2f..84d708c09bb 100644 --- a/modules/nf-core/gatk4/splitintervals/tests/main.nf.test +++ b/modules/nf-core/gatk4/splitintervals/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.multi_intervals.bed', checkIfExists: true) @@ -47,6 +48,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.interval_list', checkIfExists: true) @@ -80,6 +82,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.interval_list', checkIfExists: true) diff --git a/modules/nf-core/gatk4/splitncigarreads/tests/main.nf.test b/modules/nf-core/gatk4/splitncigarreads/tests/main.nf.test index 7a5eee0929c..fe610b457fe 100644 --- a/modules/nf-core/gatk4/splitncigarreads/tests/main.nf.test +++ b/modules/nf-core/gatk4/splitncigarreads/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), []] input[1] = [ [ id:'reference' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] input[2] = [ [ id:'reference' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) ] @@ -40,6 +41,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true)] input[1] = [ [ id:'reference' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] input[2] = [ [ id:'reference' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) ] @@ -68,6 +70,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true), [], []] input[1] = [ [ id:'reference' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] input[2] = [ [ id:'reference' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) ] diff --git a/modules/nf-core/gatk4/svannotate/tests/main.nf.test b/modules/nf-core/gatk4/svannotate/tests/main.nf.test index 57bdd7d77bb..ca0456cbeda 100644 --- a/modules/nf-core/gatk4/svannotate/tests/main.nf.test +++ b/modules/nf-core/gatk4/svannotate/tests/main.nf.test @@ -29,6 +29,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = MANTA_GERMLINE.out.diploid_sv_vcf.combine(MANTA_GERMLINE.out.diploid_sv_vcf_tbi, by:0).map({ meta, vcf, tbi -> [ meta, vcf, tbi, [] ]}) input[1] = [] input[2] = [] @@ -68,6 +69,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = MANTA_GERMLINE.out.diploid_sv_vcf.combine(MANTA_GERMLINE.out.diploid_sv_vcf_tbi, by:0).map({ meta, vcf, tbi -> [ meta, vcf, tbi, [] ]}) input[1] = Channel.value(file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)) input[2] = Channel.value(file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)) @@ -108,6 +110,7 @@ nextflow_process { when { process { """ + // testy mctestface ch_bed = Channel.of([[ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true)]) input[0] = MANTA_GERMLINE.out.diploid_sv_vcf.combine(MANTA_GERMLINE.out.diploid_sv_vcf_tbi, by:0).combine(ch_bed, by:0) diff --git a/modules/nf-core/gatk4/svcluster/tests/main.nf.test b/modules/nf-core/gatk4/svcluster/tests/main.nf.test index 6f190f758f3..6b866a85c5b 100644 --- a/modules/nf-core/gatk4/svcluster/tests/main.nf.test +++ b/modules/nf-core/gatk4/svcluster/tests/main.nf.test @@ -29,6 +29,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = MANTA_GERMLINE.out.diploid_sv_vcf.combine(MANTA_GERMLINE.out.diploid_sv_vcf_tbi, by: 0) input[1] = file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/svcluster/samples_ploidy.tsv", checkIfExists:true) input[2] = Channel.value(file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)) diff --git a/modules/nf-core/gatk4/variantfiltration/tests/main.nf.test b/modules/nf-core/gatk4/variantfiltration/tests/main.nf.test index 36b7438d392..735d0f0af9b 100644 --- a/modules/nf-core/gatk4/variantfiltration/tests/main.nf.test +++ b/modules/nf-core/gatk4/variantfiltration/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf', checkIfExists: true), @@ -51,6 +52,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true), diff --git a/modules/nf-core/gatk4/variantstotable/tests/main.nf.test b/modules/nf-core/gatk4/variantstotable/tests/main.nf.test index e6eb8207ac3..746250efadf 100644 --- a/modules/nf-core/gatk4/variantstotable/tests/main.nf.test +++ b/modules/nf-core/gatk4/variantstotable/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf', checkIfExists: true), @@ -55,6 +56,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf', checkIfExists: true), diff --git a/modules/nf-core/gatk4spark/applybqsr/tests/main.nf.test b/modules/nf-core/gatk4spark/applybqsr/tests/main.nf.test index 53f20216132..14bada69a4c 100644 --- a/modules/nf-core/gatk4spark/applybqsr/tests/main.nf.test +++ b/modules/nf-core/gatk4spark/applybqsr/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), @@ -43,6 +44,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), @@ -72,6 +74,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [], @@ -100,6 +103,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true), diff --git a/modules/nf-core/gatk4spark/markduplicates/tests/main.nf.test b/modules/nf-core/gatk4spark/markduplicates/tests/main.nf.test index 2aa2db69ed9..29b9cb06acc 100644 --- a/modules/nf-core/gatk4spark/markduplicates/tests/main.nf.test +++ b/modules/nf-core/gatk4spark/markduplicates/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) @@ -42,6 +43,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ @@ -71,6 +73,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ @@ -104,6 +107,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ @@ -134,6 +138,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [] diff --git a/modules/nf-core/gawk/tests/main.nf.test b/modules/nf-core/gawk/tests/main.nf.test index fce82ca95ad..846a99ff61a 100644 --- a/modules/nf-core/gawk/tests/main.nf.test +++ b/modules/nf-core/gawk/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) @@ -37,6 +38,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) diff --git a/modules/nf-core/gecco/run/tests/main.nf.test b/modules/nf-core/gecco/run/tests/main.nf.test index 002a8e841c1..cef4605f05e 100644 --- a/modules/nf-core/gecco/run/tests/main.nf.test +++ b/modules/nf-core/gecco/run/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/genome.fasta', checkIfExists: true), @@ -46,6 +47,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/genome.fasta', checkIfExists: true), diff --git a/modules/nf-core/gem3/gem3indexer/tests/main.nf.test b/modules/nf-core/gem3/gem3indexer/tests/main.nf.test index 706494e5547..372ef2a5501 100644 --- a/modules/nf-core/gem3/gem3indexer/tests/main.nf.test +++ b/modules/nf-core/gem3/gem3indexer/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id: 'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) @@ -35,6 +36,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id: 'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) diff --git a/modules/nf-core/gem3/gem3mapper/tests/main.nf.test b/modules/nf-core/gem3/gem3mapper/tests/main.nf.test index b6950bd352a..446983d842e 100644 --- a/modules/nf-core/gem3/gem3mapper/tests/main.nf.test +++ b/modules/nf-core/gem3/gem3mapper/tests/main.nf.test @@ -26,6 +26,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = GEM3_GEM3INDEXER.out.index input[1] = [ [ id:'test', single_end:true ], // meta map @@ -54,6 +55,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = GEM3_GEM3INDEXER.out.index input[1] = [ [ id:'test', single_end:true ], // meta map @@ -82,6 +84,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = GEM3_GEM3INDEXER.out.index input[1] = [ [ id:'test', single_end:false ], // meta map diff --git a/modules/nf-core/genmap/index/tests/main.nf.test b/modules/nf-core/genmap/index/tests/main.nf.test index 0238e42fe0e..c2d743ce813 100644 --- a/modules/nf-core/genmap/index/tests/main.nf.test +++ b/modules/nf-core/genmap/index/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id:"test"], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) @@ -37,6 +38,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id:"test"], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) diff --git a/modules/nf-core/genmod/annotate/tests/main.nf.test b/modules/nf-core/genmod/annotate/tests/main.nf.test index d17ebc9ea96..76a2a4dacbb 100644 --- a/modules/nf-core/genmod/annotate/tests/main.nf.test +++ b/modules/nf-core/genmod/annotate/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/genmod.vcf.gz', checkIfExists: true) diff --git a/modules/nf-core/genmod/compound/tests/main.nf.test b/modules/nf-core/genmod/compound/tests/main.nf.test index 43ed9f0dcf0..dd0bcf731b2 100644 --- a/modules/nf-core/genmod/compound/tests/main.nf.test +++ b/modules/nf-core/genmod/compound/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/genmod_compound.vcf', checkIfExists: true) diff --git a/modules/nf-core/genmod/models/tests/main.nf.test b/modules/nf-core/genmod/models/tests/main.nf.test index 9eba8dd5231..e3854286f69 100644 --- a/modules/nf-core/genmod/models/tests/main.nf.test +++ b/modules/nf-core/genmod/models/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/test_annotate.vcf.gz', checkIfExists: true) diff --git a/modules/nf-core/genmod/score/tests/main.nf.test b/modules/nf-core/genmod/score/tests/main.nf.test index 030ef6ba7f9..56078f59f83 100644 --- a/modules/nf-core/genmod/score/tests/main.nf.test +++ b/modules/nf-core/genmod/score/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/test_models.vcf.gz', checkIfExists: true) diff --git a/modules/nf-core/genomad/endtoend/tests/main.nf.test b/modules/nf-core/genomad/endtoend/tests/main.nf.test index 12727ffd3ea..8d413849d53 100644 --- a/modules/nf-core/genomad/endtoend/tests/main.nf.test +++ b/modules/nf-core/genomad/endtoend/tests/main.nf.test @@ -21,6 +21,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) @@ -64,6 +65,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) diff --git a/modules/nf-core/genomescope2/tests/main.nf.test b/modules/nf-core/genomescope2/tests/main.nf.test index 20c74b328ad..07dd5479ed8 100644 --- a/modules/nf-core/genomescope2/tests/main.nf.test +++ b/modules/nf-core/genomescope2/tests/main.nf.test @@ -40,6 +40,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = MERYL_HISTOGRAM.out.hist """ } @@ -69,6 +70,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = MERYL_HISTOGRAM.out.hist """ } diff --git a/modules/nf-core/geofetch/tests/main.nf.test b/modules/nf-core/geofetch/tests/main.nf.test index dbd9140aa66..e084e116a81 100644 --- a/modules/nf-core/geofetch/tests/main.nf.test +++ b/modules/nf-core/geofetch/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = 'GSE167447' """ } @@ -34,6 +35,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = 'GSE167447' """ } diff --git a/modules/nf-core/geoquery/getgeo/tests/main.nf.test b/modules/nf-core/geoquery/getgeo/tests/main.nf.test index 7debd2c0b12..cfdabfa1b5b 100644 --- a/modules/nf-core/geoquery/getgeo/tests/main.nf.test +++ b/modules/nf-core/geoquery/getgeo/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map 'GSE50790' @@ -45,6 +46,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map 'GSE50790' @@ -74,6 +76,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map 'GSE50790' diff --git a/modules/nf-core/getorganelle/config/tests/main.nf.test b/modules/nf-core/getorganelle/config/tests/main.nf.test index 6ad1cc50a96..b6b94568bdd 100644 --- a/modules/nf-core/getorganelle/config/tests/main.nf.test +++ b/modules/nf-core/getorganelle/config/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = 'all' """ @@ -56,6 +57,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = 'all' """ diff --git a/modules/nf-core/gfaffix/tests/main.nf.test b/modules/nf-core/gfaffix/tests/main.nf.test index 41fca58b64e..d2d72fb2dad 100644 --- a/modules/nf-core/gfaffix/tests/main.nf.test +++ b/modules/nf-core/gfaffix/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/gfa/assembly.gfa', checkIfExists: true) ] @@ -43,6 +44,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/gfa/assembly.gfa', checkIfExists: true) ] diff --git a/modules/nf-core/gfatools/gfa2fa/tests/main.nf.test b/modules/nf-core/gfatools/gfa2fa/tests/main.nf.test index b2bb09e101f..7ce71df4340 100644 --- a/modules/nf-core/gfatools/gfa2fa/tests/main.nf.test +++ b/modules/nf-core/gfatools/gfa2fa/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/gfa/assembly.gfa', checkIfExists: true) @@ -37,6 +38,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/gfa/assembly.gfa', checkIfExists: true) diff --git a/modules/nf-core/gfatools/stat/tests/main.nf.test b/modules/nf-core/gfatools/stat/tests/main.nf.test index 03fd6607594..37ae3007655 100644 --- a/modules/nf-core/gfatools/stat/tests/main.nf.test +++ b/modules/nf-core/gfatools/stat/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/gfa/assembly.gfa', checkIfExists: true) @@ -37,6 +38,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/gfa/assembly.gfa', checkIfExists: true) diff --git a/modules/nf-core/gffcompare/tests/main.nf.test b/modules/nf-core/gffcompare/tests/main.nf.test index 258733a9d48..3d5c17c600b 100644 --- a/modules/nf-core/gffcompare/tests/main.nf.test +++ b/modules/nf-core/gffcompare/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gff3', checkIfExists: true) ], @@ -45,6 +46,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gff3', checkIfExists: true), @@ -75,6 +77,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gff3', checkIfExists: true), diff --git a/modules/nf-core/glimpse/chunk/tests/main.nf.test b/modules/nf-core/glimpse/chunk/tests/main.nf.test index 4c278af1e60..1dd5ff48e12 100644 --- a/modules/nf-core/glimpse/chunk/tests/main.nf.test +++ b/modules/nf-core/glimpse/chunk/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'input' ], // meta map file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz'], checkIfExists: true), diff --git a/modules/nf-core/glimpse/concordance/tests/main.nf.test b/modules/nf-core/glimpse/concordance/tests/main.nf.test index 7e8505352c6..e77592858a5 100644 --- a/modules/nf-core/glimpse/concordance/tests/main.nf.test +++ b/modules/nf-core/glimpse/concordance/tests/main.nf.test @@ -54,6 +54,7 @@ nextflow_process { when { process { """ + // testy mctestface allele_freq = Channel.fromList([ file(params.modules_testdata_base_path + "delete_me/glimpse/1000GP.chr21.noNA12878.s.sites.vcf.gz",checkIfExists:true), file(params.modules_testdata_base_path + "delete_me/glimpse/1000GP.chr21.noNA12878.s.sites.vcf.gz.csi",checkIfExists:true) diff --git a/modules/nf-core/glimpse/ligate/tests/main.nf.test b/modules/nf-core/glimpse/ligate/tests/main.nf.test index 7289fc91acc..5f938e3628f 100644 --- a/modules/nf-core/glimpse/ligate/tests/main.nf.test +++ b/modules/nf-core/glimpse/ligate/tests/main.nf.test @@ -56,6 +56,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = GLIMPSE_PHASE.out.phased_variants | groupTuple() | join (BCFTOOLS_INDEX.out.csi.groupTuple()) diff --git a/modules/nf-core/glimpse/phase/tests/main.nf.test b/modules/nf-core/glimpse/phase/tests/main.nf.test index 5c92cb1fc64..2cbdd22463a 100644 --- a/modules/nf-core/glimpse/phase/tests/main.nf.test +++ b/modules/nf-core/glimpse/phase/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface ch_sample = Channel.of([sample:'present']) | combine(Channel.of('NA12878 2').collectFile(name: 'sampleinfos.txt')) | concat(Channel.of([[sample: 'absent'], []])) diff --git a/modules/nf-core/glimpse/sample/tests/main.nf.test b/modules/nf-core/glimpse/sample/tests/main.nf.test index 494c35296fe..e41e1825c87 100644 --- a/modules/nf-core/glimpse/sample/tests/main.nf.test +++ b/modules/nf-core/glimpse/sample/tests/main.nf.test @@ -46,6 +46,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = GLIMPSE_PHASE.out.phased_variants """ } diff --git a/modules/nf-core/glimpse2/chunk/tests/main.nf.test b/modules/nf-core/glimpse2/chunk/tests/main.nf.test index 0f9e8850ca1..3ee041a593e 100644 --- a/modules/nf-core/glimpse2/chunk/tests/main.nf.test +++ b/modules/nf-core/glimpse2/chunk/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/1000GP.chr21.noNA12878.s.bcf", checkIfExists: true), @@ -41,6 +42,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/1000GP.chr21.noNA12878.s.bcf", checkIfExists: true), diff --git a/modules/nf-core/glimpse2/ligate/tests/main.nf.test b/modules/nf-core/glimpse2/ligate/tests/main.nf.test index d45c448b4c8..01024618af4 100644 --- a/modules/nf-core/glimpse2/ligate/tests/main.nf.test +++ b/modules/nf-core/glimpse2/ligate/tests/main.nf.test @@ -57,6 +57,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = GLIMPSE2_PHASE.out.phased_variants | groupTuple() | join (BCFTOOLS_INDEX.out.csi.groupTuple()) diff --git a/modules/nf-core/glimpse2/phase/tests/main.nf.test b/modules/nf-core/glimpse2/phase/tests/main.nf.test index 69642590a4e..559e6636776 100644 --- a/modules/nf-core/glimpse2/phase/tests/main.nf.test +++ b/modules/nf-core/glimpse2/phase/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input_vcf = Channel.of([ [ id:'input' ], // meta map file(params.modules_testdata_base_path + "delete_me/glimpse/NA12878.chr21.s.1x.vcf.gz", checkIfExists: true), @@ -58,6 +59,7 @@ nextflow_process { when { process { """ + // testy mctestface input_bam = Channel.of([ [id:'input'], file(params.modules_testdata_base_path + "delete_me/glimpse/NA12878.chr21.s.1x.bam", checkIfExists: true), @@ -101,6 +103,7 @@ nextflow_process { when { process { """ + // testy mctestface input_cram = Channel.of([ [id:'input'], file(params.modules_testdata_base_path + "delete_me/glimpse/NA12878.chr21.s.1x.cram", checkIfExists: true), @@ -146,6 +149,7 @@ nextflow_process { when { process { """ + // testy mctestface input_bam = Channel.of([ [id:'input'], [file("https://raw.githubusercontent.com/nf-core/test-datasets/phaseimpute/data/individuals/NA12878/NA12878.s.bam", checkIfExists: true), @@ -194,6 +198,7 @@ nextflow_process { when { process { """ + // testy mctestface input_bam = Channel.of([ [id:'input'], [file("https://raw.githubusercontent.com/nf-core/test-datasets/phaseimpute/data/individuals/NA12878/NA12878.s.bam", checkIfExists: true), @@ -238,6 +243,7 @@ nextflow_process { when { process { """ + // testy mctestface input_bam = Channel.of([ [id:'input'], [file("https://raw.githubusercontent.com/nf-core/test-datasets/phaseimpute/data/individuals/NA12878/NA12878.s.1x.bcf", checkIfExists: true), diff --git a/modules/nf-core/glimpse2/splitreference/tests/main.nf.test b/modules/nf-core/glimpse2/splitreference/tests/main.nf.test index ab9ac5f9b7e..ae912a36711 100644 --- a/modules/nf-core/glimpse2/splitreference/tests/main.nf.test +++ b/modules/nf-core/glimpse2/splitreference/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'ref1000GP', single_end:false ], // meta map file(params.modules_testdata_base_path + "delete_me/glimpse/1000GP.chr21.noNA12878.s.bcf", checkIfExists: true), @@ -44,6 +45,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'ref1000GP', single_end:false ], // meta map file(params.modules_testdata_base_path + "delete_me/glimpse/1000GP.chr21.noNA12878.s.bcf", checkIfExists: true), diff --git a/modules/nf-core/gmmdemux/tests/main.nf.test b/modules/nf-core/gmmdemux/tests/main.nf.test index 674a7ce0c4f..c8639e849a4 100644 --- a/modules/nf-core/gmmdemux/tests/main.nf.test +++ b/modules/nf-core/gmmdemux/tests/main.nf.test @@ -25,6 +25,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = UNTAR.out.untar.map { meta, files -> [ [ id:'test', single_end:true ], files, "MS-11,MS-12" ] } input[1] = false input[2] = false @@ -61,6 +62,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = UNTAR.out.untar.map { meta, files -> [ [ id:'test', single_end:true ], files, "MS-11,MS-12" ] } input[1] = true input[2] = true @@ -89,6 +91,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], diff --git a/modules/nf-core/gnu/sort/tests/main.nf.test b/modules/nf-core/gnu/sort/tests/main.nf.test index e40301871b5..f748005d8b7 100644 --- a/modules/nf-core/gnu/sort/tests/main.nf.test +++ b/modules/nf-core/gnu/sort/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id:'genome_test'], file(params.test_data['generic']['unsorted_data']['unsorted_text']['genome_file'], @@ -42,6 +43,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id:'test'], file(params.test_data['generic']['unsorted_data']['unsorted_text']['intervals'], @@ -70,6 +72,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id:'test'], file(params.test_data['generic']['unsorted_data']['unsorted_text']['numbers_csv'], @@ -99,6 +102,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id:'test'], file(params.test_data['generic']['unsorted_data']['unsorted_text']['numbers_csv'], diff --git a/modules/nf-core/gnu/split/tests/main.nf.test b/modules/nf-core/gnu/split/tests/main.nf.test index 03818475a3c..fdffb5d4fcf 100644 --- a/modules/nf-core/gnu/split/tests/main.nf.test +++ b/modules/nf-core/gnu/split/tests/main.nf.test @@ -13,7 +13,8 @@ nextflow_process { config "./split_csv.config" when { process { - """ + """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'generic/csv/test.csv', checkIfExists: true) @@ -43,7 +44,8 @@ nextflow_process { config "./split_fastq_gz.config" when { process { - """ + """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_1.fastq.gz', checkIfExists: true) @@ -74,7 +76,8 @@ nextflow_process { config "./split_fastq_gz.config" when { process { - """ + """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_1.fastq.gz', checkIfExists: true) diff --git a/modules/nf-core/goat/taxonsearch/tests/main.nf.test b/modules/nf-core/goat/taxonsearch/tests/main.nf.test index c4e765adb27..8ef7abb15f7 100644 --- a/modules/nf-core/goat/taxonsearch/tests/main.nf.test +++ b/modules/nf-core/goat/taxonsearch/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test_single_species' ], // meta map 'Meles meles', @@ -39,6 +40,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test_genus_id' ], // meta map '7215', @@ -62,6 +64,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test_species' ], // meta map '', @@ -86,6 +89,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test_species' ], // meta map '', diff --git a/modules/nf-core/goleft/indexcov/tests/main.nf.test b/modules/nf-core/goleft/indexcov/tests/main.nf.test index 1296c644cd2..d3df5212fa8 100644 --- a/modules/nf-core/goleft/indexcov/tests/main.nf.test +++ b/modules/nf-core/goleft/indexcov/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test' ], // meta map [ @@ -59,6 +60,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test' ], // meta map [ @@ -105,6 +107,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test' ], // meta map [], diff --git a/modules/nf-core/goleft/indexsplit/tests/main.nf.test b/modules/nf-core/goleft/indexsplit/tests/main.nf.test index 9469e402f78..ad5dfb19927 100644 --- a/modules/nf-core/goleft/indexsplit/tests/main.nf.test +++ b/modules/nf-core/goleft/indexsplit/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.sorted.bam.bai', checkIfExists: true) @@ -43,6 +44,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.sorted.bam.bai', checkIfExists: true) diff --git a/modules/nf-core/grabix/check/tests/main.nf.test b/modules/nf-core/grabix/check/tests/main.nf.test index f8d80bb19ff..7a5071a2eb9 100644 --- a/modules/nf-core/grabix/check/tests/main.nf.test +++ b/modules/nf-core/grabix/check/tests/main.nf.test @@ -12,6 +12,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id: 'test'], // meta map [file(params.test_data_base + "/data/genomics/sarscov2/genome/genome.fasta.gz", checkIfExists: true) ] diff --git a/modules/nf-core/graphmap2/index/tests/main.nf.test b/modules/nf-core/graphmap2/index/tests/main.nf.test index c2280f4b847..91a6a659e8d 100644 --- a/modules/nf-core/graphmap2/index/tests/main.nf.test +++ b/modules/nf-core/graphmap2/index/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) """ @@ -35,6 +36,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) """ diff --git a/modules/nf-core/graphtyper/vcfconcatenate/tests/main.nf.test b/modules/nf-core/graphtyper/vcfconcatenate/tests/main.nf.test index a596539386b..54559aab155 100644 --- a/modules/nf-core/graphtyper/vcfconcatenate/tests/main.nf.test +++ b/modules/nf-core/graphtyper/vcfconcatenate/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ @@ -47,6 +48,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ diff --git a/modules/nf-core/gridss/gridss/tests/main.nf.test b/modules/nf-core/gridss/gridss/tests/main.nf.test index 610dfd5eba9..aab3fa3dc05 100644 --- a/modules/nf-core/gridss/gridss/tests/main.nf.test +++ b/modules/nf-core/gridss/gridss/tests/main.nf.test @@ -30,6 +30,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), //inputs ] @@ -59,6 +60,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), //inputs ] @@ -88,6 +90,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), //inputs ] @@ -119,6 +122,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), //inputs ] diff --git a/modules/nf-core/gstama/collapse/tests/main.nf.test b/modules/nf-core/gstama/collapse/tests/main.nf.test index 0306f827ee3..795d5ab1eb0 100644 --- a/modules/nf-core/gstama/collapse/tests/main.nf.test +++ b/modules/nf-core/gstama/collapse/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned.bam', checkIfExists: true) diff --git a/modules/nf-core/gstama/merge/tests/main.nf.test b/modules/nf-core/gstama/merge/tests/main.nf.test index c485d3eaafa..47e7e442de2 100644 --- a/modules/nf-core/gstama/merge/tests/main.nf.test +++ b/modules/nf-core/gstama/merge/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ diff --git a/modules/nf-core/gstama/polyacleanup/tests/main.nf.test b/modules/nf-core/gstama/polyacleanup/tests/main.nf.test index c447f001dc0..1303cf22a73 100644 --- a/modules/nf-core/gstama/polyacleanup/tests/main.nf.test +++ b/modules/nf-core/gstama/polyacleanup/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/transcriptome.fasta', checkIfExists: true) diff --git a/modules/nf-core/gt/gff3/tests/main.nf.test b/modules/nf-core/gt/gff3/tests/main.nf.test index 46c7da35ba7..b327631c26e 100644 --- a/modules/nf-core/gt/gff3/tests/main.nf.test +++ b/modules/nf-core/gt/gff3/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gff3', checkIfExists: true) @@ -37,6 +38,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of( '##gff-version 3', 'chr22\tID=gene:ENSG00000233995;Name=AP000547.1' diff --git a/modules/nf-core/gt/gff3validator/tests/main.nf.test b/modules/nf-core/gt/gff3validator/tests/main.nf.test index 55184f84e46..2221cfb8be0 100644 --- a/modules/nf-core/gt/gff3validator/tests/main.nf.test +++ b/modules/nf-core/gt/gff3validator/tests/main.nf.test @@ -32,6 +32,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = GT_GFF3.out.gt_gff3 """ } @@ -55,6 +56,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gff3', checkIfExists: true) @@ -77,6 +79,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gff3', checkIfExists: true) diff --git a/modules/nf-core/gt/ltrharvest/tests/main.nf.test b/modules/nf-core/gt/ltrharvest/tests/main.nf.test index f9e1ce13546..89899d3983a 100644 --- a/modules/nf-core/gt/ltrharvest/tests/main.nf.test +++ b/modules/nf-core/gt/ltrharvest/tests/main.nf.test @@ -32,6 +32,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = GT_SUFFIXERATOR.out.index """ } @@ -69,6 +70,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = GT_SUFFIXERATOR.out.index """ } @@ -106,6 +108,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = GT_SUFFIXERATOR.out.index """ } @@ -127,6 +130,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true) @@ -152,6 +156,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true) diff --git a/modules/nf-core/gt/stat/tests/main.nf.test b/modules/nf-core/gt/stat/tests/main.nf.test index 5813b540120..c9d3e6b3c4e 100644 --- a/modules/nf-core/gt/stat/tests/main.nf.test +++ b/modules/nf-core/gt/stat/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of( "##gff-version 3" + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gff3', checkIfExists: true).text.toLowerCase() @@ -41,6 +42,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id: 'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gff3', checkIfExists: true) diff --git a/modules/nf-core/gt/suffixerator/tests/main.nf.test b/modules/nf-core/gt/suffixerator/tests/main.nf.test index 3f8fb5dd512..a1ce431f029 100644 --- a/modules/nf-core/gt/suffixerator/tests/main.nf.test +++ b/modules/nf-core/gt/suffixerator/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) @@ -39,6 +40,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/proteome.fasta', checkIfExists: true) @@ -64,6 +66,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) @@ -89,6 +92,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) @@ -112,6 +116,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) @@ -137,6 +142,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) diff --git a/modules/nf-core/gtdbtk/classifywf/tests/main.nf.test b/modules/nf-core/gtdbtk/classifywf/tests/main.nf.test index deca962df93..f1eab564e7f 100644 --- a/modules/nf-core/gtdbtk/classifywf/tests/main.nf.test +++ b/modules/nf-core/gtdbtk/classifywf/tests/main.nf.test @@ -17,6 +17,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false, assembler:'SPADES' ], [ diff --git a/modules/nf-core/gtfsort/tests/main.nf.test b/modules/nf-core/gtfsort/tests/main.nf.test index fb3ee9def46..d0454bbc1f9 100644 --- a/modules/nf-core/gtfsort/tests/main.nf.test +++ b/modules/nf-core/gtfsort/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) """ } @@ -34,6 +35,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) """ } diff --git a/modules/nf-core/gubbins/tests/main.nf.test b/modules/nf-core/gubbins/tests/main.nf.test index 357d3d71d06..1f576dd9e00 100644 --- a/modules/nf-core/gubbins/tests/main.nf.test +++ b/modules/nf-core/gubbins/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/all_sites.fas', checkIfExists: true) """ @@ -46,6 +47,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/all_sites.fas', checkIfExists: true) """ diff --git a/modules/nf-core/gunc/downloaddb/tests/main.nf.test b/modules/nf-core/gunc/downloaddb/tests/main.nf.test index b719ab26f1e..fcb7d6969ce 100644 --- a/modules/nf-core/gunc/downloaddb/tests/main.nf.test +++ b/modules/nf-core/gunc/downloaddb/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = 'progenomes' """ @@ -39,6 +40,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = 'progenomes' """ diff --git a/modules/nf-core/gvcftools/extractvariants/tests/main.nf.test b/modules/nf-core/gvcftools/extractvariants/tests/main.nf.test index 9f549a58b67..55de107a553 100644 --- a/modules/nf-core/gvcftools/extractvariants/tests/main.nf.test +++ b/modules/nf-core/gvcftools/extractvariants/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true) @@ -41,6 +42,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf', checkIfExists: true) @@ -68,6 +70,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf', checkIfExists: true) diff --git a/modules/nf-core/hamronization/abricate/tests/main.nf.test b/modules/nf-core/hamronization/abricate/tests/main.nf.test index d6c21350351..4647a1d9872 100644 --- a/modules/nf-core/hamronization/abricate/tests/main.nf.test +++ b/modules/nf-core/hamronization/abricate/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:"test" ], file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/hamronization/genome.abricate.tsv', checkIfExists: true) ] input[1] = 'tsv' input[2] = '1.0.1' @@ -37,6 +38,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:"test" ], file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/hamronization/genome.abricate.tsv', checkIfExists: true) ] input[1] = 'tsv' input[2] = '1.0.1' diff --git a/modules/nf-core/hamronization/amrfinderplus/tests/main.nf.test b/modules/nf-core/hamronization/amrfinderplus/tests/main.nf.test index d74f2f56f08..9698adf5f21 100644 --- a/modules/nf-core/hamronization/amrfinderplus/tests/main.nf.test +++ b/modules/nf-core/hamronization/amrfinderplus/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/amrfinderplus/test_output.tsv", checkIfExists: true) @@ -41,6 +42,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/amrfinderplus/test_output.tsv", checkIfExists: true) diff --git a/modules/nf-core/hamronization/deeparg/tests/main.nf.test b/modules/nf-core/hamronization/deeparg/tests/main.nf.test index e13be32872e..79be7c3dbb8 100644 --- a/modules/nf-core/hamronization/deeparg/tests/main.nf.test +++ b/modules/nf-core/hamronization/deeparg/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/hamronization/genome.mapping.potential.ARG', checkIfExists: true), @@ -41,6 +42,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/hamronization/genome.mapping.potential.ARG', checkIfExists: true), diff --git a/modules/nf-core/hamronization/fargene/tests/main.nf.test b/modules/nf-core/hamronization/fargene/tests/main.nf.test index a5c5f2f7dbe..9c5a35008ca 100644 --- a/modules/nf-core/hamronization/fargene/tests/main.nf.test +++ b/modules/nf-core/hamronization/fargene/tests/main.nf.test @@ -40,6 +40,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = FARGENE.out.hmm input[1] = 'tsv' input[2] = '0.1' @@ -64,6 +65,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id: 'test'], file("dummy.fa") ] input[1] = 'tsv' input[2] = '0.1' diff --git a/modules/nf-core/hamronization/rgi/tests/main.nf.test b/modules/nf-core/hamronization/rgi/tests/main.nf.test index 52945ebe8e0..a40a981384f 100644 --- a/modules/nf-core/hamronization/rgi/tests/main.nf.test +++ b/modules/nf-core/hamronization/rgi/tests/main.nf.test @@ -57,6 +57,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = RGI_MAIN.out.tsv input[1] = 'tsv' input[2] = '1.0.2' @@ -80,6 +81,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = RGI_MAIN.out.tsv input[1] = 'tsv' input[2] = '1.0.2' diff --git a/modules/nf-core/hamronization/summarize/tests/main.nf.test b/modules/nf-core/hamronization/summarize/tests/main.nf.test index dc2da33e7f2..e2c8fe301d3 100644 --- a/modules/nf-core/hamronization/summarize/tests/main.nf.test +++ b/modules/nf-core/hamronization/summarize/tests/main.nf.test @@ -47,6 +47,7 @@ nextflow_process { when { process { """ + // testy mctestface ch_deeparg_run_one = HAMRONIZATION_DEEPARG1.out.tsv ch_deeparg_run_two = HAMRONIZATION_DEEPARG2.out.tsv @@ -79,6 +80,7 @@ nextflow_process { when { process { """ + // testy mctestface ch_deeparg_run_one = HAMRONIZATION_DEEPARG1.out.tsv ch_deeparg_run_two = HAMRONIZATION_DEEPARG2.out.tsv diff --git a/modules/nf-core/hapibd/tests/main.nf.test b/modules/nf-core/hapibd/tests/main.nf.test index 85d14460690..d2ced03d071 100644 --- a/modules/nf-core/hapibd/tests/main.nf.test +++ b/modules/nf-core/hapibd/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/hapibd/target.truth.vcf.gz", checkIfExists: true) @@ -45,6 +46,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/hapibd/target.truth.vcf.gz", checkIfExists: true) @@ -77,6 +79,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/hapibd/target.truth.vcf.gz", checkIfExists: true) diff --git a/modules/nf-core/haplocheck/tests/main.nf.test b/modules/nf-core/haplocheck/tests/main.nf.test index 8957d02e22b..cd8cbbe0064 100644 --- a/modules/nf-core/haplocheck/tests/main.nf.test +++ b/modules/nf-core/haplocheck/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_chrM.vcf.gz', checkIfExists: true) @@ -36,6 +37,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_chrM.vcf.gz', checkIfExists: true) diff --git a/modules/nf-core/haplogrep2/classify/tests/main.nf.test b/modules/nf-core/haplogrep2/classify/tests/main.nf.test index a5c42b3311b..b5a0621089d 100644 --- a/modules/nf-core/haplogrep2/classify/tests/main.nf.test +++ b/modules/nf-core/haplogrep2/classify/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_chrM.vcf.gz', checkIfExists: true) @@ -38,6 +39,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_chrM.vcf.gz', checkIfExists: true) diff --git a/modules/nf-core/happy/ftxpy/tests/main.nf.test b/modules/nf-core/happy/ftxpy/tests/main.nf.test index 12f7b225207..8a585ed38ff 100644 --- a/modules/nf-core/happy/ftxpy/tests/main.nf.test +++ b/modules/nf-core/happy/ftxpy/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz', checkIfExists: true), @@ -47,6 +48,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz', checkIfExists: true), @@ -82,6 +84,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz', checkIfExists: true), diff --git a/modules/nf-core/happy/happy/tests/main.nf.test b/modules/nf-core/happy/happy/tests/main.nf.test index a8242975215..552090d64c2 100644 --- a/modules/nf-core/happy/happy/tests/main.nf.test +++ b/modules/nf-core/happy/happy/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz', checkIfExists: true), @@ -62,6 +63,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz', checkIfExists: true), diff --git a/modules/nf-core/happy/prepy/tests/main.nf.test b/modules/nf-core/happy/prepy/tests/main.nf.test index ca79a7d8919..ee2864b442b 100644 --- a/modules/nf-core/happy/prepy/tests/main.nf.test +++ b/modules/nf-core/happy/prepy/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz', checkIfExists: true), @@ -47,6 +48,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz', checkIfExists: true), @@ -83,6 +85,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz', checkIfExists: true), diff --git a/modules/nf-core/happy/sompy/tests/main.nf.test b/modules/nf-core/happy/sompy/tests/main.nf.test index f4919c73f7b..fe5607d90c7 100644 --- a/modules/nf-core/happy/sompy/tests/main.nf.test +++ b/modules/nf-core/happy/sompy/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz', checkIfExists: true), @@ -52,6 +53,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz', checkIfExists: true), @@ -93,6 +95,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz', checkIfExists: true), diff --git a/modules/nf-core/hicap/tests/main.nf.test b/modules/nf-core/hicap/tests/main.nf.test index 7287fc79c39..1a4f41c8d0b 100644 --- a/modules/nf-core/hicap/tests/main.nf.test +++ b/modules/nf-core/hicap/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/prokaryotes/haemophilus_influenzae/genome/genome.fna.gz', checkIfExists: true) @@ -45,6 +46,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/prokaryotes/haemophilus_influenzae/genome/genome.fna.gz', checkIfExists: true) diff --git a/modules/nf-core/hmmcopy/gccounter/tests/main.nf.test b/modules/nf-core/hmmcopy/gccounter/tests/main.nf.test index f121e6f52d2..2453534a659 100644 --- a/modules/nf-core/hmmcopy/gccounter/tests/main.nf.test +++ b/modules/nf-core/hmmcopy/gccounter/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) diff --git a/modules/nf-core/hmmcopy/generatemap/tests/main.nf.test b/modules/nf-core/hmmcopy/generatemap/tests/main.nf.test index c80d95478d1..b41340811d7 100644 --- a/modules/nf-core/hmmcopy/generatemap/tests/main.nf.test +++ b/modules/nf-core/hmmcopy/generatemap/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) diff --git a/modules/nf-core/hmmcopy/mapcounter/tests/main.nf.test b/modules/nf-core/hmmcopy/mapcounter/tests/main.nf.test index 7521fb9cfb5..5b1cfb8b01a 100644 --- a/modules/nf-core/hmmcopy/mapcounter/tests/main.nf.test +++ b/modules/nf-core/hmmcopy/mapcounter/tests/main.nf.test @@ -29,6 +29,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = HMMCOPY_GENERATEMAP.out.bigwig """ } diff --git a/modules/nf-core/hmmcopy/readcounter/tests/main.nf.test b/modules/nf-core/hmmcopy/readcounter/tests/main.nf.test index 5cce3d71782..2c07fefaf42 100644 --- a/modules/nf-core/hmmcopy/readcounter/tests/main.nf.test +++ b/modules/nf-core/hmmcopy/readcounter/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam.bai', checkIfExists: true) diff --git a/modules/nf-core/hmmer/hmmbuild/tests/main.nf.test b/modules/nf-core/hmmer/hmmbuild/tests/main.nf.test index d7c058255ea..274f19f5110 100644 --- a/modules/nf-core/hmmer/hmmbuild/tests/main.nf.test +++ b/modules/nf-core/hmmer/hmmbuild/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id: 'PF14720' ], // meta map file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/hmmer/PF14720_seed.alnfaa.gz', checkIfExists: true) @@ -45,6 +46,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id: 'PF14720' ], // meta map file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/hmmer/PF14720_seed.alnfaa.gz', checkIfExists: true) diff --git a/modules/nf-core/hmmer/hmmfetch/tests/main.nf.test b/modules/nf-core/hmmer/hmmfetch/tests/main.nf.test index 46c7b58fcc2..7a3d3c750dc 100644 --- a/modules/nf-core/hmmer/hmmfetch/tests/main.nf.test +++ b/modules/nf-core/hmmer/hmmfetch/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], file('https://raw.githubusercontent.com/tseemann/barrnap/master/db/arc.hmm') @@ -40,6 +41,7 @@ nextflow_process { when { process { """ + // testy mctestface keyfile = Channel.of('16S_rRNA', '23S_rRNA').collectFile(name: 'keys.txt', newLine: true) input[0] = [ @@ -67,6 +69,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], file('https://raw.githubusercontent.com/tseemann/barrnap/master/db/arc.hmm') @@ -92,6 +95,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], file('https://raw.githubusercontent.com/tseemann/barrnap/master/db/arc.hmm') diff --git a/modules/nf-core/hmmer/hmmrank/tests/main.nf.test b/modules/nf-core/hmmer/hmmrank/tests/main.nf.test index eb1b0489517..c9661fd0465 100644 --- a/modules/nf-core/hmmer/hmmrank/tests/main.nf.test +++ b/modules/nf-core/hmmer/hmmrank/tests/main.nf.test @@ -44,6 +44,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = HMMER_HMMSEARCH.out.target_summary .collect { it[1] } .map { [ [ id: '16S-test' ], it ] } diff --git a/modules/nf-core/hmmer/hmmsearch/tests/main.nf.test b/modules/nf-core/hmmer/hmmsearch/tests/main.nf.test index f1b59e98632..6e58b650f30 100644 --- a/modules/nf-core/hmmer/hmmsearch/tests/main.nf.test +++ b/modules/nf-core/hmmer/hmmsearch/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/hmmer/bac.16S_rRNA.hmm.gz', checkIfExists: true), @@ -41,6 +42,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/hmmer/bac.16S_rRNA.hmm.gz', checkIfExists: true), @@ -74,6 +76,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/hmmer/bac.16S_rRNA.hmm.gz', checkIfExists: true), @@ -102,6 +105,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/hmmer/bac.16S_rRNA.hmm.gz', checkIfExists: true), diff --git a/modules/nf-core/homer/annotatepeaks/tests/main.nf.test b/modules/nf-core/homer/annotatepeaks/tests/main.nf.test index e54c4b90768..7522ff8ec47 100644 --- a/modules/nf-core/homer/annotatepeaks/tests/main.nf.test +++ b/modules/nf-core/homer/annotatepeaks/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) @@ -46,6 +47,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) diff --git a/modules/nf-core/homer/findpeaks/tests/main.nf.test b/modules/nf-core/homer/findpeaks/tests/main.nf.test index 4f7e100f13b..2f47c15087f 100644 --- a/modules/nf-core/homer/findpeaks/tests/main.nf.test +++ b/modules/nf-core/homer/findpeaks/tests/main.nf.test @@ -35,6 +35,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = HOMER_MAKETAGDIRECTORY.out.tagdir """ } @@ -56,6 +57,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = HOMER_MAKETAGDIRECTORY.out.tagdir """ } diff --git a/modules/nf-core/homer/maketagdirectory/tests/main.nf.test b/modules/nf-core/homer/maketagdirectory/tests/main.nf.test index 6bf570b6940..fe32d5351ab 100644 --- a/modules/nf-core/homer/maketagdirectory/tests/main.nf.test +++ b/modules/nf-core/homer/maketagdirectory/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], [ @@ -44,6 +45,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], [ @@ -73,6 +75,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], [ diff --git a/modules/nf-core/homer/pos2bed/tests/main.nf.test b/modules/nf-core/homer/pos2bed/tests/main.nf.test index 906d5719e5b..84ac9f37299 100644 --- a/modules/nf-core/homer/pos2bed/tests/main.nf.test +++ b/modules/nf-core/homer/pos2bed/tests/main.nf.test @@ -44,6 +44,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = HOMER_FINDPEAKS.out.txt """ } @@ -65,6 +66,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = HOMER_FINDPEAKS.out.txt """ } diff --git a/modules/nf-core/hpsuissero/tests/main.nf.test b/modules/nf-core/hpsuissero/tests/main.nf.test index 5e1f8b35d0e..98e53fdafe3 100644 --- a/modules/nf-core/hpsuissero/tests/main.nf.test +++ b/modules/nf-core/hpsuissero/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/prokaryotes/haemophilus_influenzae/genome/genome.fna.gz', checkIfExists: true) @@ -37,6 +38,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/prokaryotes/haemophilus_influenzae/genome/genome.fna.gz', checkIfExists: true) diff --git a/modules/nf-core/htseq/count/tests/main.nf.test b/modules/nf-core/htseq/count/tests/main.nf.test index fd70f517d05..dafdd00b021 100644 --- a/modules/nf-core/htseq/count/tests/main.nf.test +++ b/modules/nf-core/htseq/count/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), @@ -43,6 +44,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), diff --git a/modules/nf-core/htsnimtools/vcfcheck/tests/main.nf.test b/modules/nf-core/htsnimtools/vcfcheck/tests/main.nf.test index e1e87bdece6..eb705d88b9f 100644 --- a/modules/nf-core/htsnimtools/vcfcheck/tests/main.nf.test +++ b/modules/nf-core/htsnimtools/vcfcheck/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/vcf/test.vcf.gz", checkIfExists: true), @@ -49,6 +50,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/vcf/test.vcf.gz", checkIfExists: true), diff --git a/modules/nf-core/humid/tests/main.nf.test b/modules/nf-core/humid/tests/main.nf.test index 987bc20cc03..32fadea0710 100644 --- a/modules/nf-core/humid/tests/main.nf.test +++ b/modules/nf-core/humid/tests/main.nf.test @@ -61,6 +61,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), diff --git a/modules/nf-core/hypo/tests/main.nf.test b/modules/nf-core/hypo/tests/main.nf.test index 06fb15906f0..513488a618d 100644 --- a/modules/nf-core/hypo/tests/main.nf.test +++ b/modules/nf-core/hypo/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) @@ -46,6 +47,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) diff --git a/modules/nf-core/ichorcna/createpon/tests/main.nf.test b/modules/nf-core/ichorcna/createpon/tests/main.nf.test index 41ac2da8d2d..245f023af07 100644 --- a/modules/nf-core/ichorcna/createpon/tests/main.nf.test +++ b/modules/nf-core/ichorcna/createpon/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = file("https://raw.githubusercontent.com/gavinhalab/ichorCNA/master/inst/extdata/MBC_315.ctDNA.reads.wig", checkIfExists: true) input[1] = file("https://raw.githubusercontent.com/gavinhalab/ichorCNA/master/inst/extdata/gc_hg19_1000kb.wig", checkIfExists: true) input[2] = file("https://raw.githubusercontent.com/gavinhalab/ichorCNA/master/inst/extdata/map_hg19_1000kb.wig", checkIfExists: true) @@ -43,6 +44,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ file("https://raw.githubusercontent.com/gavinhalab/ichorCNA/master/inst/extdata/MBC_315.ctDNA.reads.wig", checkIfExists: true), file("https://raw.githubusercontent.com/gavinhalab/ichorCNA/master/inst/extdata/MBC_315_T2.ctDNA.reads.wig", checkIfExists: true) ] @@ -72,6 +74,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [] input[1] = [] input[2] = [] diff --git a/modules/nf-core/ichorcna/run/tests/main.nf.test b/modules/nf-core/ichorcna/run/tests/main.nf.test index 0c67ef1b0fb..63d64a23d86 100644 --- a/modules/nf-core/ichorcna/run/tests/main.nf.test +++ b/modules/nf-core/ichorcna/run/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], // meta map file("https://raw.githubusercontent.com/gavinhalab/ichorCNA/master/inst/extdata/MBC_315.ctDNA.reads.wig", checkIfExists: true) ] @@ -52,6 +53,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], // meta map file("https://raw.githubusercontent.com/gavinhalab/ichorCNA/master/inst/extdata/MBC_315.ctDNA.reads.wig", checkIfExists: true) ] diff --git a/modules/nf-core/icountmini/segment/tests/main.nf.test b/modules/nf-core/icountmini/segment/tests/main.nf.test index 794dfb34570..263b76749d5 100644 --- a/modules/nf-core/icountmini/segment/tests/main.nf.test +++ b/modules/nf-core/icountmini/segment/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/chr21_gencode.gtf', checkIfExists: true) @@ -39,6 +40,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/chr21_gencode.gtf', checkIfExists: true) diff --git a/modules/nf-core/idemux/tests/main.nf.test b/modules/nf-core/idemux/tests/main.nf.test index 9d8358addbc..586b725cb0d 100644 --- a/modules/nf-core/idemux/tests/main.nf.test +++ b/modules/nf-core/idemux/tests/main.nf.test @@ -12,7 +12,8 @@ nextflow_process { test("idemux - fastq") { when { process { - """ + """ + // testy mctestface input[0] = [ [ id:'NVQ', lane:1 ], [ @@ -44,7 +45,8 @@ nextflow_process { when { process { - """ + """ + // testy mctestface input[0] = [ [ id:'NVQ', lane:1 ], [ diff --git a/modules/nf-core/idr/tests/main.nf.test b/modules/nf-core/idr/tests/main.nf.test index 7005be87dc4..6053234b1fc 100644 --- a/modules/nf-core/idr/tests/main.nf.test +++ b/modules/nf-core/idr/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/narrowpeak/test.narrowPeak', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/narrowpeak/test2.narrowPeak', checkIfExists: true) @@ -44,6 +45,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/broadpeak/test.broadPeak', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/broadpeak/test2.broadPeak', checkIfExists: true) @@ -74,6 +76,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/narrowpeak/test.narrowPeak', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/narrowpeak/test2.narrowPeak', checkIfExists: true) @@ -105,6 +108,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/narrowpeak/test.narrowPeak', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/narrowpeak/test2.narrowPeak', checkIfExists: true) diff --git a/modules/nf-core/igv/js/tests/main.nf.test b/modules/nf-core/igv/js/tests/main.nf.test index 5710e4985e3..dece2315171 100644 --- a/modules/nf-core/igv/js/tests/main.nf.test +++ b/modules/nf-core/igv/js/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), @@ -40,6 +41,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), diff --git a/modules/nf-core/igvreports/tests/main.nf.test b/modules/nf-core/igvreports/tests/main.nf.test index ec6a86b179a..895dbe9df76 100644 --- a/modules/nf-core/igvreports/tests/main.nf.test +++ b/modules/nf-core/igvreports/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true), [], [] @@ -47,6 +48,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), @@ -83,6 +85,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], // meta map file("https://raw.githubusercontent.com/igvteam/igv-reports/master/test/data/variants/variants.vcf"), diff --git a/modules/nf-core/instrain/compare/tests/main.nf.test b/modules/nf-core/instrain/compare/tests/main.nf.test index 16617f43db1..a0a0b79fd58 100644 --- a/modules/nf-core/instrain/compare/tests/main.nf.test +++ b/modules/nf-core/instrain/compare/tests/main.nf.test @@ -32,6 +32,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of( [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) ], [ [ id:'test2' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam', checkIfExists: true) ] @@ -66,6 +67,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of( [ [ id: 'all_samples' ], [], [] ] ) input[1] = [] """ diff --git a/modules/nf-core/instrain/profile/tests/main.nf.test b/modules/nf-core/instrain/profile/tests/main.nf.test index f41b0baf776..482de4b054d 100644 --- a/modules/nf-core/instrain/profile/tests/main.nf.test +++ b/modules/nf-core/instrain/profile/tests/main.nf.test @@ -51,6 +51,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map diff --git a/modules/nf-core/interproscan/tests/main.nf.test b/modules/nf-core/interproscan/tests/main.nf.test index 1fe4625d580..f3561bade19 100644 --- a/modules/nf-core/interproscan/tests/main.nf.test +++ b/modules/nf-core/interproscan/tests/main.nf.test @@ -80,6 +80,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/proteome.fasta.gz', checkIfExists: true) diff --git a/modules/nf-core/iqtree/tests/main.nf.test b/modules/nf-core/iqtree/tests/main.nf.test index b5f2fb46a6e..a69dc462acb 100644 --- a/modules/nf-core/iqtree/tests/main.nf.test +++ b/modules/nf-core/iqtree/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id: "test" ], file("https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/setoxin.ref", checkIfExists:true), [] ] @@ -69,6 +70,7 @@ test("setoxin - treels") { when { process { """ + // testy mctestface input[0] = [ [ id: "test" ], file("https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/setoxin.ref", checkIfExists:true), [] ] @@ -126,6 +128,7 @@ test("setoxin - treels") { when { process { """ + // testy mctestface input[0] = [ [ id: "test" ], file("https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/setoxin.ref", checkIfExists:true), [] ] @@ -180,6 +183,7 @@ test("setoxin - treels") { when { process { """ + // testy mctestface input[0] = [ [ id: "test" ], [], file("https://raw.githubusercontent.com/nf-core/test-datasets/phyloplace/testdata/PF14720_seed.ft.LGCAT.newick", checkIfExists:true)] @@ -240,6 +244,7 @@ test("setoxin - treels") { when { process { """ + // testy mctestface input[0] = [ [ id: "test" ], file("https://raw.githubusercontent.com/nf-core/test-datasets/phyloplace/testdata/PF14720_seed.alnfaa", checkIfExists:true), [] ] @@ -296,6 +301,7 @@ test("setoxin - treels") { when { process { """ + // testy mctestface input[0] = [ [ id: "test" ] , [], []] input[1] = [] input[2] = [] diff --git a/modules/nf-core/islandpath/tests/main.nf.test b/modules/nf-core/islandpath/tests/main.nf.test index 7d40ee63685..80695aee66a 100644 --- a/modules/nf-core/islandpath/tests/main.nf.test +++ b/modules/nf-core/islandpath/tests/main.nf.test @@ -29,6 +29,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = GUNZIP.out.gunzip """ } diff --git a/modules/nf-core/ismapper/tests/main.nf.test b/modules/nf-core/ismapper/tests/main.nf.test index 961f887dd3e..bfd194e1672 100644 --- a/modules/nf-core/ismapper/tests/main.nf.test +++ b/modules/nf-core/ismapper/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ @@ -63,6 +64,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ diff --git a/modules/nf-core/isoseq/cluster/tests/main.nf.test b/modules/nf-core/isoseq/cluster/tests/main.nf.test index 32295fd66a5..17dd77d7122 100644 --- a/modules/nf-core/isoseq/cluster/tests/main.nf.test +++ b/modules/nf-core/isoseq/cluster/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.bam', checkIfExists: true), @@ -48,6 +49,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.bam', checkIfExists: true), diff --git a/modules/nf-core/isoseq/refine/tests/main.nf.test b/modules/nf-core/isoseq/refine/tests/main.nf.test index b1c7dda6191..3648b06db33 100644 --- a/modules/nf-core/isoseq/refine/tests/main.nf.test +++ b/modules/nf-core/isoseq/refine/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.bam', checkIfExists: true), @@ -44,6 +45,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.bam', checkIfExists: true), diff --git a/modules/nf-core/isoseq3/tag/tests/main.nf.test b/modules/nf-core/isoseq3/tag/tests/main.nf.test index 2f7816e3be8..a9f1e5390cf 100644 --- a/modules/nf-core/isoseq3/tag/tests/main.nf.test +++ b/modules/nf-core/isoseq3/tag/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'mini'], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/mini.5p--3p.bam', checkIfExists: true) @@ -42,6 +43,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'mini'], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/mini.5p--3p.bam', checkIfExists: true) diff --git a/modules/nf-core/ivar/consensus/tests/main.nf.test b/modules/nf-core/ivar/consensus/tests/main.nf.test index 9255bed082e..f8f387ab710 100644 --- a/modules/nf-core/ivar/consensus/tests/main.nf.test +++ b/modules/nf-core/ivar/consensus/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) @@ -47,6 +48,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) @@ -78,6 +80,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) diff --git a/modules/nf-core/ivar/trim/tests/main.nf.test b/modules/nf-core/ivar/trim/tests/main.nf.test index 2b96961a752..d2fd6ae4740 100644 --- a/modules/nf-core/ivar/trim/tests/main.nf.test +++ b/modules/nf-core/ivar/trim/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), @@ -46,6 +47,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), diff --git a/modules/nf-core/ivar/variants/tests/main.nf.test b/modules/nf-core/ivar/variants/tests/main.nf.test index 35a440bf5a0..e0142cbd298 100644 --- a/modules/nf-core/ivar/variants/tests/main.nf.test +++ b/modules/nf-core/ivar/variants/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) @@ -41,6 +42,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) @@ -67,6 +69,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) @@ -94,6 +97,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) diff --git a/modules/nf-core/jasminesv/tests/main.nf.test b/modules/nf-core/jasminesv/tests/main.nf.test index 851f3383e0a..11ca2c20308 100644 --- a/modules/nf-core/jasminesv/tests/main.nf.test +++ b/modules/nf-core/jasminesv/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:"test" ], [ @@ -43,6 +44,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:"test" ], [ @@ -75,6 +77,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:"test" ], [ @@ -116,6 +119,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:"test" ], [ @@ -157,6 +161,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:"test" ], [ diff --git a/modules/nf-core/jvarkit/dict2bed/tests/main.nf.test b/modules/nf-core/jvarkit/dict2bed/tests/main.nf.test index ff9eb040e35..ac4e12ce739 100644 --- a/modules/nf-core/jvarkit/dict2bed/tests/main.nf.test +++ b/modules/nf-core/jvarkit/dict2bed/tests/main.nf.test @@ -17,6 +17,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] =[ [id:"dict_test"], [ @@ -50,6 +51,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] =[ [id:"dict_stub"], [ diff --git a/modules/nf-core/jvarkit/vcf2table/tests/main.nf.test b/modules/nf-core/jvarkit/vcf2table/tests/main.nf.test index 0a0c41607cb..30e3b10f4c4 100644 --- a/modules/nf-core/jvarkit/vcf2table/tests/main.nf.test +++ b/modules/nf-core/jvarkit/vcf2table/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] =[ [id:"vcf_test"], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true), @@ -49,6 +50,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] =[ [id:"vcf_test"], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true), diff --git a/modules/nf-core/jvarkit/vcffilterjdk/tests/main.nf.test b/modules/nf-core/jvarkit/vcffilterjdk/tests/main.nf.test index 2dc0a762f1f..259b3853066 100644 --- a/modules/nf-core/jvarkit/vcffilterjdk/tests/main.nf.test +++ b/modules/nf-core/jvarkit/vcffilterjdk/tests/main.nf.test @@ -17,6 +17,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] =[ [id:"vcf_test"], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true), @@ -52,6 +53,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] =[ [id:"vcf_test"], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true), @@ -87,6 +89,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] =[ [id:"vcf_test"], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true), diff --git a/modules/nf-core/jvarkit/vcfpolyx/tests/main.nf.test b/modules/nf-core/jvarkit/vcfpolyx/tests/main.nf.test index 186ad0a9f95..ea78e0a532c 100644 --- a/modules/nf-core/jvarkit/vcfpolyx/tests/main.nf.test +++ b/modules/nf-core/jvarkit/vcfpolyx/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] =[ [id:"vcf_test"], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true), @@ -48,6 +49,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] =[ [id:"vcf_test"], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true), @@ -78,6 +80,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] =[ [id:"vcf_test"], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true), diff --git a/modules/nf-core/jvarkit/wgscoverageplotter/tests/main.nf.test b/modules/nf-core/jvarkit/wgscoverageplotter/tests/main.nf.test index f4f0d7cfcc6..183ef66e8f6 100644 --- a/modules/nf-core/jvarkit/wgscoverageplotter/tests/main.nf.test +++ b/modules/nf-core/jvarkit/wgscoverageplotter/tests/main.nf.test @@ -17,6 +17,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), @@ -48,6 +49,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] =[ [id:"test"], [], diff --git a/modules/nf-core/kaiju/kaiju/tests/main.nf.test b/modules/nf-core/kaiju/kaiju/tests/main.nf.test index ede2f952521..767bdd0714e 100644 --- a/modules/nf-core/kaiju/kaiju/tests/main.nf.test +++ b/modules/nf-core/kaiju/kaiju/tests/main.nf.test @@ -26,6 +26,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) @@ -60,6 +61,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), @@ -96,6 +98,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), diff --git a/modules/nf-core/kaiju/kaiju2krona/tests/main.nf.test b/modules/nf-core/kaiju/kaiju2krona/tests/main.nf.test index cf522cd0fa2..15d5e8760f0 100644 --- a/modules/nf-core/kaiju/kaiju2krona/tests/main.nf.test +++ b/modules/nf-core/kaiju/kaiju2krona/tests/main.nf.test @@ -87,6 +87,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = KAIJU_KAIJU.out.results input[1] = UNTAR.out.untar.map{ it[1] } """ diff --git a/modules/nf-core/kaiju/kaiju2table/tests/main.nf.test b/modules/nf-core/kaiju/kaiju2table/tests/main.nf.test index d93fb31ac41..f24852c552b 100644 --- a/modules/nf-core/kaiju/kaiju2table/tests/main.nf.test +++ b/modules/nf-core/kaiju/kaiju2table/tests/main.nf.test @@ -88,6 +88,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = KAIJU_KAIJU.out.results input[1] = UNTAR.out.untar.map{ it[1] } input[2] = 'species' diff --git a/modules/nf-core/kaiju/mergeoutputs/tests/main.nf.test b/modules/nf-core/kaiju/mergeoutputs/tests/main.nf.test index 5c2d5b3159d..5eaba813620 100644 --- a/modules/nf-core/kaiju/mergeoutputs/tests/main.nf.test +++ b/modules/nf-core/kaiju/mergeoutputs/tests/main.nf.test @@ -73,6 +73,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = KAIJU_KAIJU.out.results.join(KRAKEN2_KRAKEN2.out.classified_reads_assignment) input[1] = [ ] """ @@ -93,6 +94,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = KAIJU_KAIJU.out.results.join(KRAKEN2_KRAKEN2.out.classified_reads_assignment) input[1] = UNTAR_KAIJU.out.untar.map{ it[1] } """ @@ -115,6 +117,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = KAIJU_KAIJU.out.results.join(KRAKEN2_KRAKEN2.out.classified_reads_assignment) input[1] = [] """ diff --git a/modules/nf-core/kaiju/mkfmi/tests/main.nf.test b/modules/nf-core/kaiju/mkfmi/tests/main.nf.test index d8062b0b9f9..3fb221d9253 100644 --- a/modules/nf-core/kaiju/mkfmi/tests/main.nf.test +++ b/modules/nf-core/kaiju/mkfmi/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/proteome.fasta', checkIfExists: true) @@ -38,6 +39,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/proteome.fasta', checkIfExists: true) diff --git a/modules/nf-core/kalign/align/tests/main.nf.test b/modules/nf-core/kalign/align/tests/main.nf.test index b359439f6c4..9e65cdd4a3e 100644 --- a/modules/nf-core/kalign/align/tests/main.nf.test +++ b/modules/nf-core/kalign/align/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/contigs.fasta', checkIfExists: true) ] @@ -36,6 +37,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/contigs.fasta', checkIfExists: true) ] diff --git a/modules/nf-core/kallisto/index/tests/main.nf.test b/modules/nf-core/kallisto/index/tests/main.nf.test index eb4bc230d53..d378d3acc92 100644 --- a/modules/nf-core/kallisto/index/tests/main.nf.test +++ b/modules/nf-core/kallisto/index/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'transcriptome' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/transcriptome.fasta', checkIfExists: true) @@ -36,6 +37,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'transcriptome' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/transcriptome.fasta', checkIfExists: true) diff --git a/modules/nf-core/kallisto/quant/tests/main.nf.test b/modules/nf-core/kallisto/quant/tests/main.nf.test index 019dbea0382..579ba8f5227 100644 --- a/modules/nf-core/kallisto/quant/tests/main.nf.test +++ b/modules/nf-core/kallisto/quant/tests/main.nf.test @@ -39,6 +39,7 @@ nextflow_process { when { process { """ + // testy mctestface gtf = [] chromosomes = [] fragment_length = 150 @@ -72,6 +73,7 @@ nextflow_process { when { process { """ + // testy mctestface gtf = [] chromosomes = [] fragment_length = [] @@ -108,6 +110,7 @@ nextflow_process { when { process { """ + // testy mctestface gtf = [] chromosomes = [] fragment_length = 150 @@ -141,6 +144,7 @@ nextflow_process { when { process { """ + // testy mctestface gtf = [] chromosomes = [] fragment_length = [] diff --git a/modules/nf-core/kallistobustools/count/tests/main.nf.test b/modules/nf-core/kallistobustools/count/tests/main.nf.test index 550001f925e..bc1440523ea 100644 --- a/modules/nf-core/kallistobustools/count/tests/main.nf.test +++ b/modules/nf-core/kallistobustools/count/tests/main.nf.test @@ -28,6 +28,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of( [ [id:'test'], // meta map @@ -69,6 +70,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of( [ [id:'test'], // meta map diff --git a/modules/nf-core/kallistobustools/ref/tests/main.nf.test b/modules/nf-core/kallistobustools/ref/tests/main.nf.test index dc49d9ac5b9..331161d3630 100644 --- a/modules/nf-core/kallistobustools/ref/tests/main.nf.test +++ b/modules/nf-core/kallistobustools/ref/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) input[2] = "standard" @@ -43,6 +44,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) input[2] = "nac" @@ -74,6 +76,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) input[2] = "standard" @@ -94,6 +97,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) input[2] = "nac" diff --git a/modules/nf-core/kleborate/tests/main.nf.test b/modules/nf-core/kleborate/tests/main.nf.test index 5e0a5fcc956..da5854ce5b1 100644 --- a/modules/nf-core/kleborate/tests/main.nf.test +++ b/modules/nf-core/kleborate/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ @@ -41,6 +42,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ diff --git a/modules/nf-core/kmcp/compute/tests/main.nf.test b/modules/nf-core/kmcp/compute/tests/main.nf.test index 459e75b204d..35881cb2624 100644 --- a/modules/nf-core/kmcp/compute/tests/main.nf.test +++ b/modules/nf-core/kmcp/compute/tests/main.nf.test @@ -27,6 +27,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = UNTAR.out.untar """ } @@ -46,6 +47,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [[id:'test'],file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)] """ } @@ -67,6 +69,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [[id:'test'],file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)] """ } diff --git a/modules/nf-core/kmcp/index/tests/main.nf.test b/modules/nf-core/kmcp/index/tests/main.nf.test index a8df0bfefa1..d4bf534901a 100644 --- a/modules/nf-core/kmcp/index/tests/main.nf.test +++ b/modules/nf-core/kmcp/index/tests/main.nf.test @@ -26,6 +26,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = KMCP_COMPUTE.out.outdir """ } @@ -52,6 +53,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = KMCP_COMPUTE.out.outdir """ } diff --git a/modules/nf-core/kmcp/profile/tests/main.nf.test b/modules/nf-core/kmcp/profile/tests/main.nf.test index 20b303ed81f..921719a361f 100644 --- a/modules/nf-core/kmcp/profile/tests/main.nf.test +++ b/modules/nf-core/kmcp/profile/tests/main.nf.test @@ -66,6 +66,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = KMCP_SEARCH.out.result input[1] = UNTAR.out.untar.map{it[1]} """ @@ -91,6 +92,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = KMCP_SEARCH.out.result input[1] = UNTAR.out.untar.map{it[1]} """ diff --git a/modules/nf-core/kmcp/search/tests/main.nf.test b/modules/nf-core/kmcp/search/tests/main.nf.test index adc693e645f..32cabb43bd4 100644 --- a/modules/nf-core/kmcp/search/tests/main.nf.test +++ b/modules/nf-core/kmcp/search/tests/main.nf.test @@ -39,6 +39,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id:'test', single_end:true ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) @@ -67,6 +68,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id:'test', single_end:true ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) diff --git a/modules/nf-core/kraken2/add/tests/main.nf.test b/modules/nf-core/kraken2/add/tests/main.nf.test index 18e1a9e2474..dea93663b08 100644 --- a/modules/nf-core/kraken2/add/tests/main.nf.test +++ b/modules/nf-core/kraken2/add/tests/main.nf.test @@ -31,6 +31,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], [ @@ -66,6 +67,7 @@ test("sarscov2 protein_db stub") { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], [ diff --git a/modules/nf-core/kraken2/build/tests/main.nf.test b/modules/nf-core/kraken2/build/tests/main.nf.test index 9a8d4543b68..c6bb4f85978 100644 --- a/modules/nf-core/kraken2/build/tests/main.nf.test +++ b/modules/nf-core/kraken2/build/tests/main.nf.test @@ -53,6 +53,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = KRAKEN2_ADD.out.db input[1] = true """ @@ -82,6 +83,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = KRAKEN2_ADD.out.db input[1] = true """ diff --git a/modules/nf-core/kraken2/buildstandard/tests/main.nf.test b/modules/nf-core/kraken2/buildstandard/tests/main.nf.test index 67f3348158a..f9b982bc7bd 100644 --- a/modules/nf-core/kraken2/buildstandard/tests/main.nf.test +++ b/modules/nf-core/kraken2/buildstandard/tests/main.nf.test @@ -17,6 +17,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = true """ } diff --git a/modules/nf-core/kraken2/kraken2/tests/main.nf.test b/modules/nf-core/kraken2/kraken2/tests/main.nf.test index c0843df29ac..dea4ccaba39 100644 --- a/modules/nf-core/kraken2/kraken2/tests/main.nf.test +++ b/modules/nf-core/kraken2/kraken2/tests/main.nf.test @@ -29,6 +29,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map [ file( diff --git a/modules/nf-core/krakentools/combinekreports/tests/main.nf.test b/modules/nf-core/krakentools/combinekreports/tests/main.nf.test index b287e53b2cf..5bbb39c03b6 100644 --- a/modules/nf-core/krakentools/combinekreports/tests/main.nf.test +++ b/modules/nf-core/krakentools/combinekreports/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [id: 'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/metagenome/test_1.kraken2.report.txt', checkIfExists: true) @@ -37,6 +38,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [id: 'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/metagenome/test_1.kraken2.report.txt', checkIfExists: true) diff --git a/modules/nf-core/krakentools/extractkrakenreads/tests/main.nf.test b/modules/nf-core/krakentools/extractkrakenreads/tests/main.nf.test index a5852d96442..08e1de1aec1 100644 --- a/modules/nf-core/krakentools/extractkrakenreads/tests/main.nf.test +++ b/modules/nf-core/krakentools/extractkrakenreads/tests/main.nf.test @@ -37,6 +37,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = 2697049 input[1] = KRAKEN2_KRAKEN2.out.classified_reads_assignment input[2] = KRAKEN2_KRAKEN2.out.classified_reads_fastq @@ -84,6 +85,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = 2697049 input[1] = KRAKEN2_KRAKEN2.out.classified_reads_assignment input[2] = KRAKEN2_KRAKEN2.out.classified_reads_fastq @@ -131,6 +133,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = '2697049 694009' input[1] = KRAKEN2_KRAKEN2.out.classified_reads_assignment input[2] = KRAKEN2_KRAKEN2.out.classified_reads_fastq @@ -177,6 +180,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = 2697049 input[1] = KRAKEN2_KRAKEN2.out.classified_reads_assignment input[2] = KRAKEN2_KRAKEN2.out.classified_reads_fastq @@ -227,6 +231,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = 2697049 input[1] = KRAKEN2_KRAKEN2.out.classified_reads_assignment input[2] = KRAKEN2_KRAKEN2.out.classified_reads_fastq @@ -277,6 +282,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = '2697049 694009' input[1] = KRAKEN2_KRAKEN2.out.classified_reads_assignment input[2] = KRAKEN2_KRAKEN2.out.classified_reads_fastq diff --git a/modules/nf-core/krakentools/kreport2krona/tests/main.nf.test b/modules/nf-core/krakentools/kreport2krona/tests/main.nf.test index 1d85a0b24e7..fac8203ca42 100644 --- a/modules/nf-core/krakentools/kreport2krona/tests/main.nf.test +++ b/modules/nf-core/krakentools/kreport2krona/tests/main.nf.test @@ -50,6 +50,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = KRAKEN2_KRAKEN2.out.report """ } @@ -70,6 +71,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = KRAKEN2_KRAKEN2.out.report """ } diff --git a/modules/nf-core/krona/ktimporttaxonomy/tests/main.nf.test b/modules/nf-core/krona/ktimporttaxonomy/tests/main.nf.test index 1068f305e3e..aaec4f00b3b 100644 --- a/modules/nf-core/krona/ktimporttaxonomy/tests/main.nf.test +++ b/modules/nf-core/krona/ktimporttaxonomy/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [id: 'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/metagenome/test_1.kraken2.report.txt', checkIfExists: true) @@ -40,6 +41,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [id: 'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/metagenome/test_1.kraken2.report.txt', checkIfExists: true) diff --git a/modules/nf-core/krona/ktimporttext/tests/main.nf.test b/modules/nf-core/krona/ktimporttext/tests/main.nf.test index 79b4ce90778..c6dfb8eebcf 100644 --- a/modules/nf-core/krona/ktimporttext/tests/main.nf.test +++ b/modules/nf-core/krona/ktimporttext/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [id: 'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/metagenome/test_1.kraken2.report.txt', checkIfExists: true) @@ -36,6 +37,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [id: 'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/metagenome/test_1.kraken2.report.txt', checkIfExists: true) diff --git a/modules/nf-core/krona/ktupdatetaxonomy/tests/main.nf.test b/modules/nf-core/krona/ktupdatetaxonomy/tests/main.nf.test index 672e82d833d..81c21113d0a 100644 --- a/modules/nf-core/krona/ktupdatetaxonomy/tests/main.nf.test +++ b/modules/nf-core/krona/ktupdatetaxonomy/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface """ } @@ -38,6 +39,7 @@ nextflow_process { when { process { """ + // testy mctestface """ } diff --git a/modules/nf-core/last/dotplot/tests/main.nf.test b/modules/nf-core/last/dotplot/tests/main.nf.test index 3ea403820d2..df49f9fd680 100644 --- a/modules/nf-core/last/dotplot/tests/main.nf.test +++ b/modules/nf-core/last/dotplot/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = channel.of('NODE_1_length_20973_cov_191.628754\t2000\t2010') . collectFile(name: 'dummy_annot_b.bed', newLine: true) . map { [ @@ -44,6 +45,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/last/contigs.genome.maf.gz', checkIfExists: true), @@ -71,6 +73,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/last/contigs.genome.maf.gz', checkIfExists: true), diff --git a/modules/nf-core/last/lastal/tests/main.nf.test b/modules/nf-core/last/lastal/tests/main.nf.test index c98f07f87f7..a648052e711 100644 --- a/modules/nf-core/last/lastal/tests/main.nf.test +++ b/modules/nf-core/last/lastal/tests/main.nf.test @@ -30,6 +30,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'contigs', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/contigs.fasta', checkIfExists: true), @@ -68,6 +69,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'contigs', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/contigs.fasta', checkIfExists: true), @@ -108,6 +110,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'contigs', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/contigs.fasta', checkIfExists: true), diff --git a/modules/nf-core/last/lastdb/tests/main.nf.test b/modules/nf-core/last/lastdb/tests/main.nf.test index 1d5d403299a..9fa17b68daa 100644 --- a/modules/nf-core/last/lastdb/tests/main.nf.test +++ b/modules/nf-core/last/lastdb/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) @@ -37,6 +38,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) @@ -60,6 +62,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) diff --git a/modules/nf-core/last/mafconvert/tests/main.nf.test b/modules/nf-core/last/mafconvert/tests/main.nf.test index ea21d1f62b6..886544e8b0e 100644 --- a/modules/nf-core/last/mafconvert/tests/main.nf.test +++ b/modules/nf-core/last/mafconvert/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'contigs.genome' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/last/contigs.genome.maf.gz', checkIfExists: true) @@ -38,6 +39,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'contigs.genome' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/last/contigs.genome.maf.gz', checkIfExists: true) diff --git a/modules/nf-core/last/mafswap/tests/main.nf.test b/modules/nf-core/last/mafswap/tests/main.nf.test index ae4d7f0ae65..ee579279f55 100644 --- a/modules/nf-core/last/mafswap/tests/main.nf.test +++ b/modules/nf-core/last/mafswap/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'contigs.genome' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/last/contigs.genome.maf.gz', checkIfExists: true) @@ -37,6 +38,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'contigs.genome' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/last/contigs.genome.maf.gz', checkIfExists: true) diff --git a/modules/nf-core/last/postmask/tests/main.nf.test b/modules/nf-core/last/postmask/tests/main.nf.test index 8baf45b710f..fadb3521337 100644 --- a/modules/nf-core/last/postmask/tests/main.nf.test +++ b/modules/nf-core/last/postmask/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'sarscov2.contigs.genome' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/last/contigs.genome.maf.gz', checkIfExists: true) @@ -37,6 +38,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'sarscov2.contigs.genome' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/last/contigs.genome.maf.gz', checkIfExists: true) diff --git a/modules/nf-core/last/split/tests/main.nf.test b/modules/nf-core/last/split/tests/main.nf.test index 0e09941aabb..0d3dc0babd6 100644 --- a/modules/nf-core/last/split/tests/main.nf.test +++ b/modules/nf-core/last/split/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'sarscov.contigs.genome' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/last/contigs.genome.maf.gz', checkIfExists: true) @@ -38,6 +39,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'sarscov.contigs.genome' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/last/contigs.genome.maf.gz', checkIfExists: true) diff --git a/modules/nf-core/last/train/tests/main.nf.test b/modules/nf-core/last/train/tests/main.nf.test index 8325673ae40..7e557ae768f 100644 --- a/modules/nf-core/last/train/tests/main.nf.test +++ b/modules/nf-core/last/train/tests/main.nf.test @@ -29,6 +29,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'contigs', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/contigs.fasta', checkIfExists: true), @@ -66,6 +67,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'contigs', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/contigs.fasta', checkIfExists: true), diff --git a/modules/nf-core/learnmsa/align/tests/main.nf.test b/modules/nf-core/learnmsa/align/tests/main.nf.test index 8459ead38d5..6f9db42300d 100644 --- a/modules/nf-core/learnmsa/align/tests/main.nf.test +++ b/modules/nf-core/learnmsa/align/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.test_data['sarscov2']['genome']['informative_sites_fas'], checkIfExists: true) ] @@ -38,6 +39,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.test_data['sarscov2']['genome']['informative_sites_fas'], checkIfExists: true) ] diff --git a/modules/nf-core/legsta/tests/main.nf.test b/modules/nf-core/legsta/tests/main.nf.test index bed639db0a6..12d0c30bf8c 100644 --- a/modules/nf-core/legsta/tests/main.nf.test +++ b/modules/nf-core/legsta/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) @@ -37,6 +38,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) diff --git a/modules/nf-core/leviosam2/index/tests/main.nf.test b/modules/nf-core/leviosam2/index/tests/main.nf.test index 44d19662ec4..fb515c72d6f 100644 --- a/modules/nf-core/leviosam2/index/tests/main.nf.test +++ b/modules/nf-core/leviosam2/index/tests/main.nf.test @@ -29,6 +29,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) @@ -54,6 +55,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) diff --git a/modules/nf-core/leviosam2/lift/tests/main.nf.test b/modules/nf-core/leviosam2/lift/tests/main.nf.test index 3f2fdc4f240..ac6f55dd669 100644 --- a/modules/nf-core/leviosam2/lift/tests/main.nf.test +++ b/modules/nf-core/leviosam2/lift/tests/main.nf.test @@ -43,6 +43,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) @@ -98,6 +99,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true) @@ -128,6 +130,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) diff --git a/modules/nf-core/liftoff/tests/main.nf.test b/modules/nf-core/liftoff/tests/main.nf.test index c8ebf261ec3..22c31f2e78d 100644 --- a/modules/nf-core/liftoff/tests/main.nf.test +++ b/modules/nf-core/liftoff/tests/main.nf.test @@ -31,6 +31,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true) @@ -77,6 +78,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true) diff --git a/modules/nf-core/lima/tests/main.nf.test b/modules/nf-core/lima/tests/main.nf.test index bf7d22c2098..c1ead9a5a3e 100644 --- a/modules/nf-core/lima/tests/main.nf.test +++ b/modules/nf-core/lima/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/alz.ccs.bam', checkIfExists: true), @@ -48,6 +49,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/fasta/alz.ccs.fasta', checkIfExists: true), @@ -71,6 +73,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/fasta/alz.ccs.fasta.gz', checkIfExists: true), @@ -94,6 +97,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/fastq/alz.ccs.fastq', checkIfExists: true), @@ -117,6 +121,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/fastq/alz.ccs.fastq.gz', checkIfExists: true), @@ -142,6 +147,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/alz.ccs.bam', checkIfExists: true), @@ -167,6 +173,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/fasta/alz.ccs.fasta', checkIfExists: true), @@ -192,6 +199,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/fasta/alz.ccs.fasta.gz', checkIfExists: true), @@ -217,6 +225,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/fastq/alz.ccs.fastq', checkIfExists: true), @@ -242,6 +251,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/fastq/alz.ccs.fastq.gz', checkIfExists: true), diff --git a/modules/nf-core/lissero/tests/main.nf.test b/modules/nf-core/lissero/tests/main.nf.test index 1830a5c460d..26bf6af4366 100644 --- a/modules/nf-core/lissero/tests/main.nf.test +++ b/modules/nf-core/lissero/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file("https://github.com/MDU-PHL/LisSero/raw/master/tests/test_seq/NC_002973.fna", checkIfExists: true) ] @@ -39,6 +40,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file("https://github.com/MDU-PHL/LisSero/raw/master/tests/test_seq/NC_002973.fna", checkIfExists: true) ] diff --git a/modules/nf-core/lofreq/alnqual/tests/main.nf.test b/modules/nf-core/lofreq/alnqual/tests/main.nf.test index bfa08324098..a30c412262a 100644 --- a/modules/nf-core/lofreq/alnqual/tests/main.nf.test +++ b/modules/nf-core/lofreq/alnqual/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) @@ -44,6 +45,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) diff --git a/modules/nf-core/lofreq/call/tests/main.nf.test b/modules/nf-core/lofreq/call/tests/main.nf.test index 208df18d60b..b5f6c7855fa 100644 --- a/modules/nf-core/lofreq/call/tests/main.nf.test +++ b/modules/nf-core/lofreq/call/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true), @@ -43,6 +44,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true), @@ -72,6 +74,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true), diff --git a/modules/nf-core/lofreq/callparallel/tests/main.nf.test b/modules/nf-core/lofreq/callparallel/tests/main.nf.test index 31f199208b3..01971278aae 100644 --- a/modules/nf-core/lofreq/callparallel/tests/main.nf.test +++ b/modules/nf-core/lofreq/callparallel/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), @@ -47,6 +48,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), @@ -82,6 +84,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), diff --git a/modules/nf-core/lofreq/filter/tests/main.nf.test b/modules/nf-core/lofreq/filter/tests/main.nf.test index bff32a8948b..7f480169c76 100644 --- a/modules/nf-core/lofreq/filter/tests/main.nf.test +++ b/modules/nf-core/lofreq/filter/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'testvcf' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) @@ -33,6 +34,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'testvcf' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true) @@ -56,6 +58,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'testvcf' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true) ] diff --git a/modules/nf-core/lofreq/indelqual/tests/main.nf.test b/modules/nf-core/lofreq/indelqual/tests/main.nf.test index 3771f22f563..e9f03243453 100644 --- a/modules/nf-core/lofreq/indelqual/tests/main.nf.test +++ b/modules/nf-core/lofreq/indelqual/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) @@ -47,6 +48,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) diff --git a/modules/nf-core/lofreq/somatic/tests/main.nf.test b/modules/nf-core/lofreq/somatic/tests/main.nf.test index 4109fee3f60..e7ab54b9a75 100644 --- a/modules/nf-core/lofreq/somatic/tests/main.nf.test +++ b/modules/nf-core/lofreq/somatic/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam', checkIfExists: true), @@ -55,6 +56,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam', checkIfExists: true), diff --git a/modules/nf-core/lofreq/viterbi/tests/main.nf.test b/modules/nf-core/lofreq/viterbi/tests/main.nf.test index 1e5d6033512..39d75f49688 100644 --- a/modules/nf-core/lofreq/viterbi/tests/main.nf.test +++ b/modules/nf-core/lofreq/viterbi/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) @@ -42,6 +43,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) diff --git a/modules/nf-core/longphase/haplotag/tests/main.nf.test b/modules/nf-core/longphase/haplotag/tests/main.nf.test index c80133c6d0b..bf07df37337 100644 --- a/modules/nf-core/longphase/haplotag/tests/main.nf.test +++ b/modules/nf-core/longphase/haplotag/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam', checkIfExists: true), @@ -54,6 +55,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam', checkIfExists: true), @@ -94,6 +96,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam', checkIfExists: true), @@ -134,6 +137,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam', checkIfExists: true), @@ -171,6 +175,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam', checkIfExists: true), diff --git a/modules/nf-core/longphase/phase/tests/main.nf.test b/modules/nf-core/longphase/phase/tests/main.nf.test index 3e303312bef..5024e989832 100644 --- a/modules/nf-core/longphase/phase/tests/main.nf.test +++ b/modules/nf-core/longphase/phase/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam', checkIfExists: true), @@ -49,6 +50,7 @@ test("[ bam, bai, snps, svs, [] ], fasta, fai") { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam', checkIfExists: true), @@ -83,6 +85,7 @@ test("[ bam x2, bai x2, snps, svs, [] ], fasta, fai") { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], [ @@ -125,6 +128,7 @@ test("[ bam x2, bai x2, snps, svs, [] ], fasta, fai") { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam', checkIfExists: true), diff --git a/modules/nf-core/ltrfinder/tests/main.nf.test b/modules/nf-core/ltrfinder/tests/main.nf.test index dc8c8033d35..498d118887d 100644 --- a/modules/nf-core/ltrfinder/tests/main.nf.test +++ b/modules/nf-core/ltrfinder/tests/main.nf.test @@ -29,6 +29,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = GUNZIP.out.gunzip """ } @@ -48,6 +49,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) @@ -72,6 +74,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/eukaryotes/actinidia_chinensis/genome/chr1/genome.fasta.gz', checkIfExists: true) diff --git a/modules/nf-core/ltrharvest/tests/main.nf.test b/modules/nf-core/ltrharvest/tests/main.nf.test index e200fdef6a2..5f33cea4fd7 100644 --- a/modules/nf-core/ltrharvest/tests/main.nf.test +++ b/modules/nf-core/ltrharvest/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true) @@ -40,6 +41,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) @@ -69,6 +71,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) diff --git a/modules/nf-core/ltrretriever/lai/tests/main.nf.test b/modules/nf-core/ltrretriever/lai/tests/main.nf.test index 69294910aad..f20454d62cc 100644 --- a/modules/nf-core/ltrretriever/lai/tests/main.nf.test +++ b/modules/nf-core/ltrretriever/lai/tests/main.nf.test @@ -80,6 +80,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = GUNZIP.out.gunzip input[1] = LTRRETRIEVER_LTRRETRIEVER.out.pass_list.map { meta, pass_list -> pass_list } input[2] = LTRRETRIEVER_LTRRETRIEVER.out.annotation_out.map { meta, annotation_out -> annotation_out } @@ -108,6 +109,7 @@ nextflow_process { when { process { """ + // testy mctestface def pass_list = new File('test.pass.list') def out_file = new File('test.out') def monoploid_seqs = new File('some_seqs.list.txt') @@ -139,6 +141,7 @@ nextflow_process { when { process { """ + // testy mctestface def pass_list = new File('test.pass.list') def out_file = new File('test.out') def monoploid_seqs = new File('some_seqs.list.txt') diff --git a/modules/nf-core/ltrretriever/ltrretriever/tests/main.nf.test b/modules/nf-core/ltrretriever/ltrretriever/tests/main.nf.test index 4d512f3693d..99705195b10 100644 --- a/modules/nf-core/ltrretriever/ltrretriever/tests/main.nf.test +++ b/modules/nf-core/ltrretriever/ltrretriever/tests/main.nf.test @@ -58,6 +58,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = input[0] = [ [ id: 'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) @@ -131,6 +132,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = GUNZIP.out.gunzip input[1] = CAT_CAT.out.file_out.map { meta, tabout -> tabout } input[2] = [] @@ -162,6 +164,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/eukaryotes/actinidia_chinensis/genome/chr1/genome.fasta.gz', checkIfExists: true) diff --git a/modules/nf-core/macrel/contigs/tests/main.nf.test b/modules/nf-core/macrel/contigs/tests/main.nf.test index 5b641b1ea57..1e72c786819 100644 --- a/modules/nf-core/macrel/contigs/tests/main.nf.test +++ b/modules/nf-core/macrel/contigs/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/fasta/test1.contigs.fa.gz', checkIfExists: true) @@ -46,6 +47,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/fasta/test1.contigs.fa.gz', checkIfExists: true) diff --git a/modules/nf-core/macs2/callpeak/tests/main.nf.test b/modules/nf-core/macs2/callpeak/tests/main.nf.test index 4ab8ceb12e6..b61845bf632 100644 --- a/modules/nf-core/macs2/callpeak/tests/main.nf.test +++ b/modules/nf-core/macs2/callpeak/tests/main.nf.test @@ -91,6 +91,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) ], diff --git a/modules/nf-core/macs3/callpeak/tests/main.nf.test b/modules/nf-core/macs3/callpeak/tests/main.nf.test index 4338c96b8c5..06d06e7de16 100644 --- a/modules/nf-core/macs3/callpeak/tests/main.nf.test +++ b/modules/nf-core/macs3/callpeak/tests/main.nf.test @@ -91,6 +91,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) ], diff --git a/modules/nf-core/mafft/tests/main.nf.test b/modules/nf-core/mafft/tests/main.nf.test index 683979f7af0..5a1e7029c5e 100644 --- a/modules/nf-core/mafft/tests/main.nf.test +++ b/modules/nf-core/mafft/tests/main.nf.test @@ -11,6 +11,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/scaffolds.fasta', checkIfExists: true) @@ -38,6 +39,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/scaffolds.fasta', checkIfExists: true) @@ -66,6 +68,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) @@ -95,6 +98,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) @@ -125,6 +129,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) @@ -155,6 +160,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) @@ -185,6 +191,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) @@ -216,6 +223,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) diff --git a/modules/nf-core/mageck/count/tests/main.nf.test b/modules/nf-core/mageck/count/tests/main.nf.test index fbfeaeb641f..c44e08f01c8 100644 --- a/modules/nf-core/mageck/count/tests/main.nf.test +++ b/modules/nf-core/mageck/count/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test,test2', single_end:true] , // meta map [file(params.modules_testdata_base_path + 'genomics/mus_musculus/mageck/ERR376998.small.fastq.gz', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/mus_musculus/mageck/ERR376999.small.fastq.gz', checkIfExists: true)] @@ -39,6 +40,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test,test2', single_end:true] , // meta map [file(params.modules_testdata_base_path + 'genomics/mus_musculus/mageck/ERR376998.small.fastq.gz', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/mus_musculus/mageck/ERR376999.small.fastq.gz', checkIfExists: true)] diff --git a/modules/nf-core/mageck/mle/tests/main.nf.test b/modules/nf-core/mageck/mle/tests/main.nf.test index f6d06280485..82e37a1d717 100644 --- a/modules/nf-core/mageck/mle/tests/main.nf.test +++ b/modules/nf-core/mageck/mle/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/mus_musculus/mageck/count_table.csv', checkIfExists: true) @@ -43,6 +44,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/mus_musculus/mageck/count_table.csv', checkIfExists: true) diff --git a/modules/nf-core/mageck/test/tests/main.nf.test b/modules/nf-core/mageck/test/tests/main.nf.test index 45cb37345f6..85cc370948a 100644 --- a/modules/nf-core/mageck/test/tests/main.nf.test +++ b/modules/nf-core/mageck/test/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/mus_musculus/mageck/count_table.csv', checkIfExists: true) ] @@ -45,6 +46,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/mus_musculus/mageck/count_table.csv', checkIfExists: true) ] @@ -73,6 +75,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/mus_musculus/mageck/count_table.csv', checkIfExists: true) ] diff --git a/modules/nf-core/magus/align/tests/main.nf.test b/modules/nf-core/magus/align/tests/main.nf.test index 6b603f2074b..94b74ea848e 100644 --- a/modules/nf-core/magus/align/tests/main.nf.test +++ b/modules/nf-core/magus/align/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file("https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true) ] @@ -45,6 +46,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file("https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true) ] @@ -87,6 +89,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file("https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true) ] diff --git a/modules/nf-core/magus/guidetree/tests/main.nf.test b/modules/nf-core/magus/guidetree/tests/main.nf.test index 953e37e5cfa..07e21051a7a 100644 --- a/modules/nf-core/magus/guidetree/tests/main.nf.test +++ b/modules/nf-core/magus/guidetree/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file("https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true) ] diff --git a/modules/nf-core/malt/build/tests/main.nf.test b/modules/nf-core/malt/build/tests/main.nf.test index 229460271c6..db8ab052756 100644 --- a/modules/nf-core/malt/build/tests/main.nf.test +++ b/modules/nf-core/malt/build/tests/main.nf.test @@ -27,6 +27,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.fasta", checkIfExists: true) input[1] = [] input[2] = UNZIP.out.unzipped_archive.map { it[1] } @@ -65,6 +66,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.fasta", checkIfExists: true) input[1] = [] input[2] = UNZIP.out.unzipped_archive.map { it[1] } diff --git a/modules/nf-core/malt/run/tests/main.nf.test b/modules/nf-core/malt/run/tests/main.nf.test index 304c01d4a21..e08b78b6d21 100644 --- a/modules/nf-core/malt/run/tests/main.nf.test +++ b/modules/nf-core/malt/run/tests/main.nf.test @@ -38,6 +38,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test_1', single_end:false ], [ @@ -71,6 +72,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test_1', single_end:false ], [ diff --git a/modules/nf-core/maltextract/tests/main.nf.test b/modules/nf-core/maltextract/tests/main.nf.test index 0cc9701d126..680a3c1f7ea 100644 --- a/modules/nf-core/maltextract/tests/main.nf.test +++ b/modules/nf-core/maltextract/tests/main.nf.test @@ -24,6 +24,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [], // meta map file(params.modules_testdata_base_path + 'delete_me/malt/test.rma6') ] diff --git a/modules/nf-core/manta/convertinversion/tests/main.nf.test b/modules/nf-core/manta/convertinversion/tests/main.nf.test index 58adf6e3ad1..16bbbb49180 100644 --- a/modules/nf-core/manta/convertinversion/tests/main.nf.test +++ b/modules/nf-core/manta/convertinversion/tests/main.nf.test @@ -42,6 +42,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = MANTA_TUMORONLY.out.tumor_sv_vcf input[1] = [ [ id:'fasta' ], @@ -71,6 +72,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = MANTA_TUMORONLY.out.tumor_sv_vcf input[1] = [ [ id:'fasta' ], diff --git a/modules/nf-core/manta/germline/tests/main.nf.test b/modules/nf-core/manta/germline/tests/main.nf.test index 1d49ad23a19..9679f9af6a0 100644 --- a/modules/nf-core/manta/germline/tests/main.nf.test +++ b/modules/nf-core/manta/germline/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true), @@ -52,6 +53,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'bed_test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true), @@ -89,6 +91,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'bed_test', single_end:false ], // meta map [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test2.paired_end.sorted.cram', checkIfExists: true) @@ -131,6 +134,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true), diff --git a/modules/nf-core/manta/somatic/tests/main.nf.test b/modules/nf-core/manta/somatic/tests/main.nf.test index 121f13849f4..8fd431ff613 100644 --- a/modules/nf-core/manta/somatic/tests/main.nf.test +++ b/modules/nf-core/manta/somatic/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram.crai', checkIfExists: true), @@ -51,6 +52,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'bed_test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram.crai', checkIfExists: true), @@ -90,6 +92,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram.crai', checkIfExists: true), diff --git a/modules/nf-core/manta/tumoronly/tests/main.nf.test b/modules/nf-core/manta/tumoronly/tests/main.nf.test index 9d57b1d8f7f..e28bb663251 100644 --- a/modules/nf-core/manta/tumoronly/tests/main.nf.test +++ b/modules/nf-core/manta/tumoronly/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test2.paired_end.recalibrated.sorted.cram', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test2.paired_end.recalibrated.sorted.cram.crai', checkIfExists: true), @@ -51,6 +52,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'bed_test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test2.paired_end.recalibrated.sorted.cram', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test2.paired_end.recalibrated.sorted.cram.crai', checkIfExists: true), @@ -90,6 +92,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test2.paired_end.recalibrated.sorted.cram', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test2.paired_end.recalibrated.sorted.cram.crai', checkIfExists: true), diff --git a/modules/nf-core/mapad/index/tests/main.nf.test b/modules/nf-core/mapad/index/tests/main.nf.test index 7bb3f43b93a..50d2a07b4a4 100644 --- a/modules/nf-core/mapad/index/tests/main.nf.test +++ b/modules/nf-core/mapad/index/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id: 'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) diff --git a/modules/nf-core/mapad/map/tests/main.nf.test b/modules/nf-core/mapad/map/tests/main.nf.test index d240f231b44..61347e10894 100644 --- a/modules/nf-core/mapad/map/tests/main.nf.test +++ b/modules/nf-core/mapad/map/tests/main.nf.test @@ -28,6 +28,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:true ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.bam', checkIfExists: true) ]) diff --git a/modules/nf-core/mapdamage2/tests/main.nf.test b/modules/nf-core/mapdamage2/tests/main.nf.test index 5c3e1a42bc4..e5375ff049b 100644 --- a/modules/nf-core/mapdamage2/tests/main.nf.test +++ b/modules/nf-core/mapdamage2/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) @@ -59,6 +60,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) diff --git a/modules/nf-core/mash/dist/tests/main.nf.test b/modules/nf-core/mash/dist/tests/main.nf.test index 31d5296ba04..dd72a51ada2 100644 --- a/modules/nf-core/mash/dist/tests/main.nf.test +++ b/modules/nf-core/mash/dist/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/contigs.fasta', checkIfExists: true) @@ -39,6 +40,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/contigs.fasta', checkIfExists: true) diff --git a/modules/nf-core/mash/screen/tests/main.nf.test b/modules/nf-core/mash/screen/tests/main.nf.test index 6152beafbbf..17bb5fa5e15 100644 --- a/modules/nf-core/mash/screen/tests/main.nf.test +++ b/modules/nf-core/mash/screen/tests/main.nf.test @@ -29,6 +29,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false], // meta map @@ -72,6 +73,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false], // meta map diff --git a/modules/nf-core/mash/sketch/tests/main.nf.test b/modules/nf-core/mash/sketch/tests/main.nf.test index c73e314492d..4ad055d24b8 100644 --- a/modules/nf-core/mash/sketch/tests/main.nf.test +++ b/modules/nf-core/mash/sketch/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false], // meta map @@ -41,6 +42,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false], // meta map diff --git a/modules/nf-core/mashmap/tests/main.nf.test b/modules/nf-core/mashmap/tests/main.nf.test index afcfc24df6b..0a4190b105e 100644 --- a/modules/nf-core/mashmap/tests/main.nf.test +++ b/modules/nf-core/mashmap/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface // Query input[0] = [ [ id:'test', single_end:false ], @@ -43,6 +44,7 @@ nextflow_process { when { process { """ + // testy mctestface // Query input[0] = [ [ id:'test', single_end:false ], diff --git a/modules/nf-core/mashtree/tests/main.nf.test b/modules/nf-core/mashtree/tests/main.nf.test index 3b4aca46101..236e0df7729 100644 --- a/modules/nf-core/mashtree/tests/main.nf.test +++ b/modules/nf-core/mashtree/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ @@ -45,6 +46,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ diff --git a/modules/nf-core/maxbin2/tests/main.nf.test b/modules/nf-core/maxbin2/tests/main.nf.test index efb23c2b159..3eba3865308 100644 --- a/modules/nf-core/maxbin2/tests/main.nf.test +++ b/modules/nf-core/maxbin2/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test1', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/fasta/test1.contigs.fa.gz', checkIfExists: true), diff --git a/modules/nf-core/mcquant/tests/main.nf.test b/modules/nf-core/mcquant/tests/main.nf.test index 055a67e77d0..ba159c89926 100644 --- a/modules/nf-core/mcquant/tests/main.nf.test +++ b/modules/nf-core/mcquant/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'image' ], // meta map file(params.modules_testdata_base_path + 'imaging/quantification/cycif_tonsil_registered.ome.tif', checkIfExists: true) @@ -47,6 +48,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'image' ], // meta map file(params.modules_testdata_base_path + 'imaging/quantification/cycif_tonsil_registered.ome.tif', checkIfExists: true) diff --git a/modules/nf-core/mcroni/tests/main.nf.test b/modules/nf-core/mcroni/tests/main.nf.test index 10c0f89445f..4e58851843b 100644 --- a/modules/nf-core/mcroni/tests/main.nf.test +++ b/modules/nf-core/mcroni/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) @@ -37,6 +38,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) diff --git a/modules/nf-core/mcstaging/imc2mc/tests/main.nf.test b/modules/nf-core/mcstaging/imc2mc/tests/main.nf.test index 8967070adf8..6c2d48f8793 100644 --- a/modules/nf-core/mcstaging/imc2mc/tests/main.nf.test +++ b/modules/nf-core/mcstaging/imc2mc/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'imaging/staging/imaging_mass_cytometry/acquisition.txt', checkIfExists: true), @@ -39,6 +40,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'imaging/staging/imaging_mass_cytometry/acquisition.txt', checkIfExists: true), diff --git a/modules/nf-core/mcstaging/phenoimager2mc/tests/main.nf.test b/modules/nf-core/mcstaging/phenoimager2mc/tests/main.nf.test index 2ed83e82cc8..bb7ec5c1ac9 100644 --- a/modules/nf-core/mcstaging/phenoimager2mc/tests/main.nf.test +++ b/modules/nf-core/mcstaging/phenoimager2mc/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface // define inputs of the process here. Example: input[0] = [ [ id:'test' ], @@ -42,6 +43,7 @@ test("phenoimager2mc - tif - stub") { when { process { """ + // testy mctestface // define inputs of the process here. Example: input[0] = [ [ id:'test' ], diff --git a/modules/nf-core/md5sum/tests/main.nf.test b/modules/nf-core/md5sum/tests/main.nf.test index a6f7cf8614b..2be26e4b534 100644 --- a/modules/nf-core/md5sum/tests/main.nf.test +++ b/modules/nf-core/md5sum/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id: 'hello' ], [ file(params.modules_testdata_base_path + 'generic/txt/hello.txt', checkIfExists: true) ] @@ -37,6 +38,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id: 'hello' ], [ file(params.modules_testdata_base_path + 'generic/txt/hello.txt', checkIfExists: true) ] @@ -59,6 +61,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id: 'hello' ], [ file(params.modules_testdata_base_path + 'generic/txt/hello.txt', checkIfExists: true) ] @@ -81,6 +84,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id: 'test' ], [ @@ -106,6 +110,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id: 'test' ], [ @@ -132,6 +137,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id: 'test' ], [ @@ -157,6 +163,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id: 'test' ], [ diff --git a/modules/nf-core/medaka/tests/main.nf.test b/modules/nf-core/medaka/tests/main.nf.test index 948e398c824..51cf866af26 100644 --- a/modules/nf-core/medaka/tests/main.nf.test +++ b/modules/nf-core/medaka/tests/main.nf.test @@ -12,6 +12,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/nanopore/fastq/test.fastq.gz', checkIfExists: true), diff --git a/modules/nf-core/megahit/tests/main.nf.test b/modules/nf-core/megahit/tests/main.nf.test index b52765d433e..30c729e2a2d 100644 --- a/modules/nf-core/megahit/tests/main.nf.test +++ b/modules/nf-core/megahit/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id:"test", single_end:true], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), []] @@ -43,6 +44,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id:"test", single_end:false], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) @@ -74,6 +76,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id:"test", single_end:false], [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_1.fastq.gz', checkIfExists: true)] , [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_2.fastq.gz', checkIfExists: true)] @@ -107,6 +110,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id:"test", single_end:true], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), [] diff --git a/modules/nf-core/megan/rma2info/tests/main.nf.test b/modules/nf-core/megan/rma2info/tests/main.nf.test index 3a3c807a24b..c555b2fe7cb 100644 --- a/modules/nf-core/megan/rma2info/tests/main.nf.test +++ b/modules/nf-core/megan/rma2info/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'delete_me/malt/test.rma6', checkIfExists: true) @@ -43,6 +44,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'delete_me/malt/test.rma6', checkIfExists: true) diff --git a/modules/nf-core/meningotype/tests/main.nf.test b/modules/nf-core/meningotype/tests/main.nf.test index 98c63b5ee07..8c7626fdf47 100644 --- a/modules/nf-core/meningotype/tests/main.nf.test +++ b/modules/nf-core/meningotype/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] @@ -35,6 +36,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] diff --git a/modules/nf-core/merfin/hist/tests/main.nf.test b/modules/nf-core/merfin/hist/tests/main.nf.test index 7b392f1c610..8513f6f52bf 100644 --- a/modules/nf-core/merfin/hist/tests/main.nf.test +++ b/modules/nf-core/merfin/hist/tests/main.nf.test @@ -50,6 +50,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + '/genomics/sarscov2/genome/genome.fasta', checkIfExists: true) @@ -114,6 +115,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + '/genomics/sarscov2/genome/genome.fasta', checkIfExists: true) @@ -215,6 +217,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + '/genomics/sarscov2/genome/genome.fasta', checkIfExists: true) @@ -319,6 +322,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + '/genomics/sarscov2/genome/genome.fasta', checkIfExists: true) @@ -428,6 +432,7 @@ nextflow_process { when { process { """ + // testy mctestface Channel.from([ [ id:'test_sars', single_end:false ], // meta map file(params.modules_testdata_base_path + '/genomics/sarscov2/genome/genome.fasta', checkIfExists: true) @@ -557,6 +562,7 @@ nextflow_process { when { process { """ + // testy mctestface Channel.from([ [ id:'test_sars', single_end:false ], // meta map file(params.modules_testdata_base_path + '/genomics/sarscov2/genome/genome.fasta', checkIfExists: true) diff --git a/modules/nf-core/merqury/hapmers/tests/main.nf.test b/modules/nf-core/merqury/hapmers/tests/main.nf.test index 8dcfa0d6585..dd7dee69825 100644 --- a/modules/nf-core/merqury/hapmers/tests/main.nf.test +++ b/modules/nf-core/merqury/hapmers/tests/main.nf.test @@ -56,6 +56,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = MERYL_COUNT.out.meryl_db input[1] = MERYL_COUNT_MATERNAL.out.meryl_db.map { meta, db -> db } input[2] = MERYL_COUNT_PATERNAL.out.meryl_db.map { meta, db -> db } @@ -86,6 +87,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = MERYL_COUNT.out.meryl_db input[1] = MERYL_COUNT_MATERNAL.out.meryl_db.map { meta, db -> db } input[2] = MERYL_COUNT_PATERNAL.out.meryl_db.map { meta, db -> db } diff --git a/modules/nf-core/merqury/merqury/tests/main.nf.test b/modules/nf-core/merqury/merqury/tests/main.nf.test index 46a07c02a41..f0b4ca73966 100644 --- a/modules/nf-core/merqury/merqury/tests/main.nf.test +++ b/modules/nf-core/merqury/merqury/tests/main.nf.test @@ -44,6 +44,7 @@ nextflow_process { when { process { """ + // testy mctestface assembly = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) @@ -118,6 +119,7 @@ nextflow_process { when { process { """ + // testy mctestface ch_assembly = Channel.value([ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) @@ -168,6 +170,7 @@ nextflow_process { when { process { """ + // testy mctestface assembly = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) diff --git a/modules/nf-core/merquryfk/merquryfk/tests/main.nf.test b/modules/nf-core/merquryfk/merquryfk/tests/main.nf.test index c46843c6d68..4341ffd456e 100644 --- a/modules/nf-core/merquryfk/merquryfk/tests/main.nf.test +++ b/modules/nf-core/merquryfk/merquryfk/tests/main.nf.test @@ -53,6 +53,7 @@ nextflow_process { when { process { """ + // testy mctestface assembly = [ [ id:'test', single_end:true ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) @@ -82,6 +83,7 @@ nextflow_process { when { process { """ + // testy mctestface assembly = [ [ id:'test', single_end:true ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) @@ -110,7 +112,8 @@ nextflow_process { config "./nextflow.trio.config" when { process { - """ + """ + // testy mctestface assembly = [ [ id:'test', single_end:true ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) @@ -141,6 +144,7 @@ nextflow_process { when { process { """ + // testy mctestface assembly = [ [ id:'test', single_end:true ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) diff --git a/modules/nf-core/meryl/count/tests/main.nf.test b/modules/nf-core/meryl/count/tests/main.nf.test index cce46c363e7..b28872abfcb 100644 --- a/modules/nf-core/meryl/count/tests/main.nf.test +++ b/modules/nf-core/meryl/count/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.value([ [ id: 'test', single_end: true ], // meta map file( params.modules_testdata_base_path + "/genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test1_1.fastq.gz", checkIfExists: true ) @@ -39,6 +40,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.value([ [ id: 'test', single_end: true ], // meta map file( params.modules_testdata_base_path + "/genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test1_1.fastq.gz", checkIfExists: true ) diff --git a/modules/nf-core/meryl/histogram/tests/main.nf.test b/modules/nf-core/meryl/histogram/tests/main.nf.test index 307fa39b4a5..39bc24f3862 100644 --- a/modules/nf-core/meryl/histogram/tests/main.nf.test +++ b/modules/nf-core/meryl/histogram/tests/main.nf.test @@ -30,6 +30,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = MERYL_COUNT.out.meryl_db input[1] = Channel.value(21) """ @@ -52,6 +53,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = MERYL_COUNT.out.meryl_db input[1] = Channel.value(21) """ diff --git a/modules/nf-core/meryl/unionsum/tests/main.nf.test b/modules/nf-core/meryl/unionsum/tests/main.nf.test index dc1bf8afa0b..56edd45f441 100644 --- a/modules/nf-core/meryl/unionsum/tests/main.nf.test +++ b/modules/nf-core/meryl/unionsum/tests/main.nf.test @@ -30,6 +30,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = MERYL_COUNT.out.meryl_db input[1] = Channel.value(21) """ @@ -68,6 +69,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = MERYL_COUNT.out.meryl_db input[1] = Channel.value(21) """ @@ -105,6 +107,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = MERYL_COUNT.out.meryl_db input[1] = Channel.value(21) """ diff --git a/modules/nf-core/metabat2/jgisummarizebamcontigdepths/tests/main.nf.test b/modules/nf-core/metabat2/jgisummarizebamcontigdepths/tests/main.nf.test index d4852ba5b06..f3d65296450 100644 --- a/modules/nf-core/metabat2/jgisummarizebamcontigdepths/tests/main.nf.test +++ b/modules/nf-core/metabat2/jgisummarizebamcontigdepths/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), @@ -39,6 +40,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), diff --git a/modules/nf-core/metamaps/classify/tests/main.nf.test b/modules/nf-core/metamaps/classify/tests/main.nf.test index 81357bc23ce..5d57baa4477 100644 --- a/modules/nf-core/metamaps/classify/tests/main.nf.test +++ b/modules/nf-core/metamaps/classify/tests/main.nf.test @@ -41,6 +41,7 @@ nextflow_process { when { process { """ + // testy mctestface classification_folder = METAMAPS_MAPDIRECTLY.out.classification_res .join(METAMAPS_MAPDIRECTLY.out.meta_file) .join(METAMAPS_MAPDIRECTLY.out.meta_unmappedreadsLengths) @@ -95,6 +96,7 @@ nextflow_process { when { process { """ + // testy mctestface classification_folder = METAMAPS_MAPDIRECTLY.out.classification_res .join(METAMAPS_MAPDIRECTLY.out.meta_file) .join(METAMAPS_MAPDIRECTLY.out.meta_unmappedreadsLengths) diff --git a/modules/nf-core/metamaps/mapdirectly/tests/main.nf.test b/modules/nf-core/metamaps/mapdirectly/tests/main.nf.test index 7368a3e8302..575759f7dc4 100644 --- a/modules/nf-core/metamaps/mapdirectly/tests/main.nf.test +++ b/modules/nf-core/metamaps/mapdirectly/tests/main.nf.test @@ -29,6 +29,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/nanopore/fastq/test.fastq.gz', checkIfExists: true) @@ -69,6 +70,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/nanopore/fastq/test.fastq.gz', checkIfExists: true) diff --git a/modules/nf-core/metaphlan/makedb/tests/main.nf.test b/modules/nf-core/metaphlan/makedb/tests/main.nf.test index 00b65852879..9adf41b90d7 100644 --- a/modules/nf-core/metaphlan/makedb/tests/main.nf.test +++ b/modules/nf-core/metaphlan/makedb/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface """ } } @@ -37,6 +38,7 @@ nextflow_process { when { process { """ + // testy mctestface """ } } diff --git a/modules/nf-core/metaphlan/mergemetaphlantables/tests/main.nf.test b/modules/nf-core/metaphlan/mergemetaphlantables/tests/main.nf.test index 17e9400cab5..28e66863efa 100644 --- a/modules/nf-core/metaphlan/mergemetaphlantables/tests/main.nf.test +++ b/modules/nf-core/metaphlan/mergemetaphlantables/tests/main.nf.test @@ -43,6 +43,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = METAPHLAN_METAPHLAN.out.profile.map{meta, profile -> [[id: 'test'], profile]}.groupTuple() """ } @@ -64,6 +65,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = METAPHLAN_METAPHLAN.out.profile.map{meta, profile -> [[id: 'test'], profile]}.groupTuple() """ } diff --git a/modules/nf-core/metaphlan/metaphlan/tests/main.nf.test b/modules/nf-core/metaphlan/metaphlan/tests/main.nf.test index dff5cf7132c..df21526ceb9 100644 --- a/modules/nf-core/metaphlan/metaphlan/tests/main.nf.test +++ b/modules/nf-core/metaphlan/metaphlan/tests/main.nf.test @@ -30,6 +30,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:true ], // meta map file( params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz',checkIfExists: true ) @@ -58,6 +59,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map [ file( params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz',checkIfExists: true ), @@ -87,6 +89,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:true ], // meta map file( params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/contigs.fasta',checkIfExists: true ) @@ -116,6 +119,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map [ file( params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz',checkIfExists: true ), diff --git a/modules/nf-core/methyldackel/extract/tests/main.nf.test b/modules/nf-core/methyldackel/extract/tests/main.nf.test index 562f5c2e368..02f843e8d0e 100644 --- a/modules/nf-core/methyldackel/extract/tests/main.nf.test +++ b/modules/nf-core/methyldackel/extract/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam.bai', checkIfExists: true) @@ -40,6 +41,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam', checkIfExists: true), @@ -67,6 +69,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam', checkIfExists: true), diff --git a/modules/nf-core/methyldackel/mbias/tests/main.nf.test b/modules/nf-core/methyldackel/mbias/tests/main.nf.test index 14c30df714a..0b6e2309271 100644 --- a/modules/nf-core/methyldackel/mbias/tests/main.nf.test +++ b/modules/nf-core/methyldackel/mbias/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam', checkIfExists: true), @@ -45,6 +46,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam', checkIfExists: true), diff --git a/modules/nf-core/mindagap/duplicatefinder/tests/main.nf.test b/modules/nf-core/mindagap/duplicatefinder/tests/main.nf.test index d43a7de8358..d1dcbb729b0 100644 --- a/modules/nf-core/mindagap/duplicatefinder/tests/main.nf.test +++ b/modules/nf-core/mindagap/duplicatefinder/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], // meta map file('https://raw.githubusercontent.com/nf-core/test-datasets/molkart/test_data/input_data/spots.txt') diff --git a/modules/nf-core/mindagap/mindagap/tests/main.nf.test b/modules/nf-core/mindagap/mindagap/tests/main.nf.test index dbad49101be..d4cd8a49b6b 100644 --- a/modules/nf-core/mindagap/mindagap/tests/main.nf.test +++ b/modules/nf-core/mindagap/mindagap/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file(params.test_data['imaging']['tiff']['mouse_heart_wga'], checkIfExists: true) diff --git a/modules/nf-core/minia/tests/main.nf.test b/modules/nf-core/minia/tests/main.nf.test index e83a74c0f78..04d55246b9d 100644 --- a/modules/nf-core/minia/tests/main.nf.test +++ b/modules/nf-core/minia/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ @@ -48,6 +49,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ diff --git a/modules/nf-core/miniasm/tests/main.nf.test b/modules/nf-core/miniasm/tests/main.nf.test index ee7498a12c1..4ed8276ea40 100644 --- a/modules/nf-core/miniasm/tests/main.nf.test +++ b/modules/nf-core/miniasm/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/nanopore/fastq/test.fastq.gz', checkIfExists: true), @@ -37,6 +38,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/nanopore/fastq/test.fastq.gz', checkIfExists: true), diff --git a/modules/nf-core/minimap2/align/tests/main.nf.test b/modules/nf-core/minimap2/align/tests/main.nf.test index 4072c171979..d3e1f4d7b22 100644 --- a/modules/nf-core/minimap2/align/tests/main.nf.test +++ b/modules/nf-core/minimap2/align/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) @@ -48,6 +49,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) @@ -83,6 +85,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ @@ -120,6 +123,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), @@ -154,6 +158,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test3.single_end.markduplicates.sorted.bam', checkIfExists: true) @@ -188,6 +193,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test3.single_end.markduplicates.sorted.bam', checkIfExists: true) @@ -223,6 +229,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test3.single_end.markduplicates.sorted.bam', checkIfExists: true) @@ -254,6 +261,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) @@ -286,6 +294,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) @@ -318,6 +327,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) @@ -350,6 +360,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test3.single_end.markduplicates.sorted.bam', checkIfExists: true) @@ -382,6 +393,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test3.single_end.markduplicates.sorted.bam', checkIfExists: true) @@ -414,6 +426,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test3.single_end.markduplicates.sorted.bam', checkIfExists: true) diff --git a/modules/nf-core/minimap2/index/tests/main.nf.test b/modules/nf-core/minimap2/index/tests/main.nf.test index 97840ff75d0..3eac05c2506 100644 --- a/modules/nf-core/minimap2/index/tests/main.nf.test +++ b/modules/nf-core/minimap2/index/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) diff --git a/modules/nf-core/miniprot/align/tests/main.nf.test b/modules/nf-core/miniprot/align/tests/main.nf.test index 12366934ace..53d94cdf2c8 100644 --- a/modules/nf-core/miniprot/align/tests/main.nf.test +++ b/modules/nf-core/miniprot/align/tests/main.nf.test @@ -29,6 +29,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/proteome.fasta', checkIfExists: true)] input[1] = MINIPROT_INDEX.out.index @@ -50,6 +51,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/proteome.fasta', checkIfExists: true)] input[1] = MINIPROT_INDEX.out.index @@ -71,6 +73,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/proteome.fasta', checkIfExists: true)] input[1] = MINIPROT_INDEX.out.index diff --git a/modules/nf-core/miniprot/index/tests/main.nf.test b/modules/nf-core/miniprot/index/tests/main.nf.test index b6092df97e5..d675fa24fc9 100644 --- a/modules/nf-core/miniprot/index/tests/main.nf.test +++ b/modules/nf-core/miniprot/index/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] """ @@ -34,6 +35,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] """ diff --git a/modules/nf-core/miranda/tests/main.nf.test b/modules/nf-core/miranda/tests/main.nf.test index d2851388c11..1a382fd5253 100644 --- a/modules/nf-core/miranda/tests/main.nf.test +++ b/modules/nf-core/miranda/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'cel_N2_1' ], file("https://raw.githubusercontent.com/nf-core/test-datasets/circrna/miranda/cel_N2_1.fa") @@ -45,6 +46,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'cel_N2_1' ], file("https://raw.githubusercontent.com/nf-core/test-datasets/circrna/miranda/cel_N2_1.fa") diff --git a/modules/nf-core/mirdeep2/mapper/tests/main.nf.test b/modules/nf-core/mirdeep2/mapper/tests/main.nf.test index 62e3e615abc..9cb415e2751 100644 --- a/modules/nf-core/mirdeep2/mapper/tests/main.nf.test +++ b/modules/nf-core/mirdeep2/mapper/tests/main.nf.test @@ -57,6 +57,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test_reads', single_end:false ], // meta map file('https://github.com/rajewsky-lab/mirdeep2/raw/master/tutorial_dir/reads.fa', checkIfExists: true) @@ -92,6 +93,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = SEQKIT_REPLACE.out.fastx input[1] = BOWTIE_BUILD.out.index """ @@ -120,6 +122,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test_reads', single_end:false ], // meta map file('https://github.com/rajewsky-lab/mirdeep2/raw/master/tutorial_dir/reads.fa', checkIfExists: true) diff --git a/modules/nf-core/mirdeep2/mirdeep2/tests/main.nf.test b/modules/nf-core/mirdeep2/mirdeep2/tests/main.nf.test index b7b73ec123d..881793433b9 100644 --- a/modules/nf-core/mirdeep2/mirdeep2/tests/main.nf.test +++ b/modules/nf-core/mirdeep2/mirdeep2/tests/main.nf.test @@ -47,6 +47,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = MIRDEEP2_MAPPER.out.outputs input[1] = [ [ id:'genome_cel_cluster' ], // meta map @@ -84,6 +85,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = MIRDEEP2_MAPPER.out.outputs input[1] = [ [ id:'genome_cel_cluster' ], // meta map diff --git a/modules/nf-core/mirtop/counts/tests/main.nf.test b/modules/nf-core/mirtop/counts/tests/main.nf.test index 5048c166ab8..131b4096437 100644 --- a/modules/nf-core/mirtop/counts/tests/main.nf.test +++ b/modules/nf-core/mirtop/counts/tests/main.nf.test @@ -38,6 +38,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = MIRTOP_GFF.out.gff input[1] = [ [ id:'hairpin'], // meta map @@ -67,6 +68,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = MIRTOP_GFF.out.gff input[1] = [ [ id:'hairpin'], // meta map diff --git a/modules/nf-core/mirtop/export/tests/main.nf.test b/modules/nf-core/mirtop/export/tests/main.nf.test index 234caf57303..772951b7172 100644 --- a/modules/nf-core/mirtop/export/tests/main.nf.test +++ b/modules/nf-core/mirtop/export/tests/main.nf.test @@ -37,6 +37,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = MIRTOP_GFF.out.gff input[1] = [ [ id:'hairpin'], // meta map @@ -66,6 +67,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = MIRTOP_GFF.out.gff input[1] = [ [ id:'hairpin'], // meta map diff --git a/modules/nf-core/mirtop/gff/tests/main.nf.test b/modules/nf-core/mirtop/gff/tests/main.nf.test index 85977b43665..1fb88907456 100644 --- a/modules/nf-core/mirtop/gff/tests/main.nf.test +++ b/modules/nf-core/mirtop/gff/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'sample_sim_isomir_bam'], // meta map file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/mirtop/sim_isomir_sort.bam", checkIfExists: true), @@ -46,6 +47,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'sample_sim_isomir_bam'], // meta map file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/mirtop/sim_isomir_sort.bam", checkIfExists: true), diff --git a/modules/nf-core/mirtop/stats/tests/main.nf.test b/modules/nf-core/mirtop/stats/tests/main.nf.test index e9d16cdcc2b..85b354158ce 100644 --- a/modules/nf-core/mirtop/stats/tests/main.nf.test +++ b/modules/nf-core/mirtop/stats/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'mirtop_gff_sample1'], // meta map file("https://github.com/miRTop/mirtop/raw/master/data/examples/gff/correct_file.gff", checkIfExists: true), @@ -39,6 +40,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'mirtop_gff_sample1'], // meta map file("https://github.com/miRTop/mirtop/raw/master/data/examples/gff/correct_file.gff", checkIfExists: true), diff --git a/modules/nf-core/mirtrace/qc/tests/main.nf.test b/modules/nf-core/mirtrace/qc/tests/main.nf.test index d0ef1c7b3bd..e5337a2dadb 100644 --- a/modules/nf-core/mirtrace/qc/tests/main.nf.test +++ b/modules/nf-core/mirtrace/qc/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ @@ -58,6 +59,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ @@ -84,6 +86,7 @@ nextflow_process { when { process { """ + // testy mctestface ch_reads = Channel.of([ [ id:'test' ], // meta map [ diff --git a/modules/nf-core/mmseqs/createdb/tests/main.nf.test b/modules/nf-core/mmseqs/createdb/tests/main.nf.test index d4a4f0c8bff..d4284949976 100644 --- a/modules/nf-core/mmseqs/createdb/tests/main.nf.test +++ b/modules/nf-core/mmseqs/createdb/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/contigs.fasta', checkIfExists: true) @@ -39,6 +40,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], diff --git a/modules/nf-core/mmseqs/createindex/tests/main.nf.test b/modules/nf-core/mmseqs/createindex/tests/main.nf.test index 30bcc92760a..09cc9aa6fa1 100644 --- a/modules/nf-core/mmseqs/createindex/tests/main.nf.test +++ b/modules/nf-core/mmseqs/createindex/tests/main.nf.test @@ -26,6 +26,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = UNTAR.out.untar """ } diff --git a/modules/nf-core/mmseqs/createtsv/tests/main.nf.test b/modules/nf-core/mmseqs/createtsv/tests/main.nf.test index 1aa7463d4f6..8ed64180042 100644 --- a/modules/nf-core/mmseqs/createtsv/tests/main.nf.test +++ b/modules/nf-core/mmseqs/createtsv/tests/main.nf.test @@ -50,6 +50,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = MMSEQS_TAXONOMY.out.db_taxonomy input[1] = [[:],[]] input[2] = MMSEQS_TAXA.out.db @@ -166,6 +167,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = MMSEQS_TAXONOMY.out.db_taxonomy input[1] = [[:],[]] input[2] = MMSEQS_TAXA.out.db diff --git a/modules/nf-core/mmseqs/databases/tests/main.nf.test b/modules/nf-core/mmseqs/databases/tests/main.nf.test index 3fe5d20069d..aa5ff8b2466 100644 --- a/modules/nf-core/mmseqs/databases/tests/main.nf.test +++ b/modules/nf-core/mmseqs/databases/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = "SILVA" """ @@ -38,6 +39,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = "SILVA" """ diff --git a/modules/nf-core/mmseqs/linclust/tests/main.nf.test b/modules/nf-core/mmseqs/linclust/tests/main.nf.test index 9a3b6de1788..72ed30769e3 100644 --- a/modules/nf-core/mmseqs/linclust/tests/main.nf.test +++ b/modules/nf-core/mmseqs/linclust/tests/main.nf.test @@ -26,6 +26,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = UNTAR.out.untar """ } diff --git a/modules/nf-core/mmseqs/taxonomy/tests/main.nf.test b/modules/nf-core/mmseqs/taxonomy/tests/main.nf.test index 95f1bc22e62..1956f270fb8 100644 --- a/modules/nf-core/mmseqs/taxonomy/tests/main.nf.test +++ b/modules/nf-core/mmseqs/taxonomy/tests/main.nf.test @@ -39,6 +39,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = MMSEQS_CREATEDB.out.db input[1] = MMSEQS_DATABASES.out.database """ @@ -64,6 +65,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = MMSEQS_CREATEDB.out.db input[1] = MMSEQS_DATABASES.out.database """ diff --git a/modules/nf-core/mobsuite/recon/tests/main.nf.test b/modules/nf-core/mobsuite/recon/tests/main.nf.test index 23301fa85a3..855f5f2ace1 100644 --- a/modules/nf-core/mobsuite/recon/tests/main.nf.test +++ b/modules/nf-core/mobsuite/recon/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) @@ -38,6 +39,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) diff --git a/modules/nf-core/modkit/pileup/tests/main.nf.test b/modules/nf-core/modkit/pileup/tests/main.nf.test index 371cc3b94d4..2e2d4f1a1c3 100644 --- a/modules/nf-core/modkit/pileup/tests/main.nf.test +++ b/modules/nf-core/modkit/pileup/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id: 'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.phased.bam', checkIfExists: true), @@ -38,6 +39,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id: 'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.phased.bam', checkIfExists: true), @@ -66,6 +68,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id: 'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.phased.bam', checkIfExists: true), @@ -98,6 +101,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id: 'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.phased.bam', checkIfExists: true), @@ -130,6 +134,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id: 'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.phased.bam', checkIfExists: true), @@ -162,6 +167,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id: 'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.phased.bam', checkIfExists: true), @@ -194,6 +200,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id: 'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.phased.bam', checkIfExists: true), @@ -221,6 +228,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id: 'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.phased.bam', checkIfExists: true), @@ -251,6 +259,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id: 'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.phased.bam', checkIfExists: true), @@ -284,6 +293,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id: 'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.phased.bam', checkIfExists: true), @@ -317,6 +327,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id: 'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.phased.bam', checkIfExists: true), @@ -350,6 +361,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id: 'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.phased.bam', checkIfExists: true), diff --git a/modules/nf-core/molkartgarage/clahe/tests/main.nf.test b/modules/nf-core/molkartgarage/clahe/tests/main.nf.test index 291b7fb7213..9a9e9eabeac 100644 --- a/modules/nf-core/molkartgarage/clahe/tests/main.nf.test +++ b/modules/nf-core/molkartgarage/clahe/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'imaging/tiff/mindagap.mouse_heart.wga.tiff', checkIfExists: true) @@ -41,6 +42,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'imaging/tiff/mindagap.mouse_heart.wga.tiff', checkIfExists: true) diff --git a/modules/nf-core/mosdepth/tests/main.nf.test b/modules/nf-core/mosdepth/tests/main.nf.test index 0b3c860d321..4852eefe83e 100644 --- a/modules/nf-core/mosdepth/tests/main.nf.test +++ b/modules/nf-core/mosdepth/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), @@ -38,6 +39,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), @@ -63,6 +65,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), @@ -91,6 +94,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), @@ -120,6 +124,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), @@ -146,6 +151,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), @@ -172,6 +178,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), @@ -198,6 +205,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), @@ -223,6 +231,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), diff --git a/modules/nf-core/motus/profile/tests/main.nf.test b/modules/nf-core/motus/profile/tests/main.nf.test index b0f041086cc..18bb3080907 100644 --- a/modules/nf-core/motus/profile/tests/main.nf.test +++ b/modules/nf-core/motus/profile/tests/main.nf.test @@ -27,6 +27,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ @@ -70,6 +71,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file( params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true )] @@ -98,6 +100,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map file( params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true ) @@ -122,6 +125,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ @@ -149,6 +153,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file( params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true )] diff --git a/modules/nf-core/msisensor2/scan/tests/main.nf.test b/modules/nf-core/msisensor2/scan/tests/main.nf.test index 0814efa36b2..feb9da86868 100644 --- a/modules/nf-core/msisensor2/scan/tests/main.nf.test +++ b/modules/nf-core/msisensor2/scan/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome2.fasta', checkIfExists: true) @@ -39,6 +40,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome2.fasta', checkIfExists: true) diff --git a/modules/nf-core/msisensorpro/scan/tests/main.nf.test b/modules/nf-core/msisensorpro/scan/tests/main.nf.test index 38334ac2217..7414a088468 100644 --- a/modules/nf-core/msisensorpro/scan/tests/main.nf.test +++ b/modules/nf-core/msisensorpro/scan/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true) @@ -38,6 +39,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true) diff --git a/modules/nf-core/mtnucratio/tests/main.nf.test b/modules/nf-core/mtnucratio/tests/main.nf.test index 97975b3dca9..4fea6a860ba 100644 --- a/modules/nf-core/mtnucratio/tests/main.nf.test +++ b/modules/nf-core/mtnucratio/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.sorted.bam', checkIfExists: true)] input[1] = 'mt_id' @@ -36,6 +37,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.sorted.bam', checkIfExists: true)] input[1] = 'mt_id' diff --git a/modules/nf-core/mudskipper/bulk/tests/main.nf.test b/modules/nf-core/mudskipper/bulk/tests/main.nf.test index f8bcdef0a83..498c9463565 100644 --- a/modules/nf-core/mudskipper/bulk/tests/main.nf.test +++ b/modules/nf-core/mudskipper/bulk/tests/main.nf.test @@ -32,6 +32,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = SAMTOOLS_SORT.out.bam input[1] = [] input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) @@ -78,6 +79,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = SAMTOOLS_SORT.out.bam input[1] = MUDSKIPPER_INDEX.out.index input[2] = [] diff --git a/modules/nf-core/mudskipper/index/tests/main.nf.test b/modules/nf-core/mudskipper/index/tests/main.nf.test index 1f5b886a794..99389f968e6 100644 --- a/modules/nf-core/mudskipper/index/tests/main.nf.test +++ b/modules/nf-core/mudskipper/index/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) """ } diff --git a/modules/nf-core/multiqc/tests/main.nf.test b/modules/nf-core/multiqc/tests/main.nf.test index 33316a7ddb3..04b7d23c4d5 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test +++ b/modules/nf-core/multiqc/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true)) input[1] = [] input[2] = [] @@ -41,6 +42,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true)) input[1] = Channel.of(file("https://github.com/nf-core/tools/raw/dev/nf_core/pipeline-template/assets/multiqc_config.yml", checkIfExists: true)) input[2] = [] @@ -68,6 +70,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true)) input[1] = [] input[2] = [] diff --git a/modules/nf-core/multivcfanalyzer/tests/main.nf.test b/modules/nf-core/multivcfanalyzer/tests/main.nf.test index 7d610ad8c0c..f965678d9ce 100644 --- a/modules/nf-core/multivcfanalyzer/tests/main.nf.test +++ b/modules/nf-core/multivcfanalyzer/tests/main.nf.test @@ -55,6 +55,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = GUNZIP.out.gunzip.collect{ meta, vcf -> vcf }.map{ vcf -> [[ id: 'testVCF'], vcf]} input[1] = [ [] , file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) @@ -100,6 +101,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = GUNZIP.out.gunzip.collect{ meta, vcf -> vcf }.map{ vcf -> [[ id: 'testVCF'], vcf]} input[1] = [ [] , file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) diff --git a/modules/nf-core/mygene/tests/main.nf.test b/modules/nf-core/mygene/tests/main.nf.test index e5ba64caa3b..decdda7e7f5 100644 --- a/modules/nf-core/mygene/tests/main.nf.test +++ b/modules/nf-core/mygene/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id : 'test'], file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/mus_musculus/rnaseq_expression/SRP254919.gene_meta.tsv") @@ -39,6 +40,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id : 'test'], file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/mus_musculus/rnaseq_expression/SRP254919.gene_meta.tsv") @@ -64,6 +66,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id : 'test'], file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/mus_musculus/rnaseq_expression/SRP254919.gene_meta.tsv") @@ -88,6 +91,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id : 'test'], file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/mus_musculus/rnaseq_expression/SRP254919.gene_meta.tsv") diff --git a/modules/nf-core/mykrobe/predict/tests/main.nf.test b/modules/nf-core/mykrobe/predict/tests/main.nf.test index 0bef07ca1d4..0643a64e0c1 100644 --- a/modules/nf-core/mykrobe/predict/tests/main.nf.test +++ b/modules/nf-core/mykrobe/predict/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) @@ -45,6 +46,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) diff --git a/modules/nf-core/nanocomp/tests/main.nf.test b/modules/nf-core/nanocomp/tests/main.nf.test index c8fcbccf164..8c5d5a54bd5 100644 --- a/modules/nf-core/nanocomp/tests/main.nf.test +++ b/modules/nf-core/nanocomp/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id: "test_" ], [ file(params.modules_testdata_base_path + 'genomics/sarscov2/nanopore/fastq/test.fastq.gz', checkIfExists: true) ] ] """ @@ -58,6 +59,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id: "test_"] , [ file(params.modules_testdata_base_path + 'genomics/sarscov2/nanopore/sequencing_summary/test.sequencing_summary.txt', checkIfExists: true) ] ] """ @@ -102,6 +104,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id: "test_" ], [ file(params.modules_testdata_base_path + 'genomics/sarscov2/nanopore/sequencing_summary/test.sequencing_summary.txt', checkIfExists: true) ] ] """ diff --git a/modules/nf-core/nanofilt/tests/main.nf.test b/modules/nf-core/nanofilt/tests/main.nf.test index 13be95e483e..85ed19e2b8d 100644 --- a/modules/nf-core/nanofilt/tests/main.nf.test +++ b/modules/nf-core/nanofilt/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/nanopore/fastq/test.fastq.gz', checkIfExists: true) @@ -42,6 +43,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/nanopore/fastq/test.fastq.gz', checkIfExists: true) diff --git a/modules/nf-core/nanolyse/tests/main.nf.test b/modules/nf-core/nanolyse/tests/main.nf.test index 651cc03d3a0..5e3bcb6f142 100644 --- a/modules/nf-core/nanolyse/tests/main.nf.test +++ b/modules/nf-core/nanolyse/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/nanopore/fastq/test.fastq.gz', checkIfExists: true) ] @@ -44,6 +45,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/nanopore/fastq/test.fastq.gz', checkIfExists: true) ] diff --git a/modules/nf-core/nanoplot/tests/main.nf.test b/modules/nf-core/nanoplot/tests/main.nf.test index 233b6cc7dbc..5109784b81b 100644 --- a/modules/nf-core/nanoplot/tests/main.nf.test +++ b/modules/nf-core/nanoplot/tests/main.nf.test @@ -12,6 +12,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/nanopore/sequencing_summary/test.sequencing_summary.txt', checkIfExists: true) ] @@ -42,6 +43,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/nanopore/fastq/test.fastq.gz', checkIfExists: true) ] @@ -73,6 +75,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/nanopore/sequencing_summary/test.sequencing_summary.txt', checkIfExists: true) ] diff --git a/modules/nf-core/nanoq/tests/main.nf.test b/modules/nf-core/nanoq/tests/main.nf.test index ef63d12f737..7af26d7b9db 100644 --- a/modules/nf-core/nanoq/tests/main.nf.test +++ b/modules/nf-core/nanoq/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/nanopore/fastq/test.fastq.gz', checkIfExists: true) @@ -36,6 +37,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/nanopore/fastq/test.fastq.gz', checkIfExists: true) @@ -57,6 +59,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/nanopore/fastq/test.fastq.gz', checkIfExists: true) @@ -78,6 +81,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/nanopore/fastq/test.fastq.gz', checkIfExists: true) @@ -102,6 +106,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/nanopore/fastq/test.fastq.gz', checkIfExists: true) diff --git a/modules/nf-core/narfmap/align/tests/main.nf.test b/modules/nf-core/narfmap/align/tests/main.nf.test index a920339b4fe..c6a5471abb6 100644 --- a/modules/nf-core/narfmap/align/tests/main.nf.test +++ b/modules/nf-core/narfmap/align/tests/main.nf.test @@ -28,6 +28,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) @@ -58,6 +59,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) @@ -88,6 +90,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ @@ -121,6 +124,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ @@ -154,6 +158,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ @@ -189,6 +194,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ @@ -221,6 +227,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) diff --git a/modules/nf-core/narfmap/align/tests/segfault.nf.test b/modules/nf-core/narfmap/align/tests/segfault.nf.test index 14e101d809b..7bf5351ebd9 100644 --- a/modules/nf-core/narfmap/align/tests/segfault.nf.test +++ b/modules/nf-core/narfmap/align/tests/segfault.nf.test @@ -30,6 +30,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map file('https://raw.githubusercontent.com/nf-core/test-datasets/nascent/testdata/SRX882903_T2.fastq.gz', checkIfExists: true) diff --git a/modules/nf-core/ncbigenomedownload/tests/main.nf.test b/modules/nf-core/ncbigenomedownload/tests/main.nf.test index fd759b4d22f..a249b993e8b 100644 --- a/modules/nf-core/ncbigenomedownload/tests/main.nf.test +++ b/modules/nf-core/ncbigenomedownload/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ] ] input[1] = [] input[2] = [] diff --git a/modules/nf-core/nextclade/datasetget/tests/main.nf.test b/modules/nf-core/nextclade/datasetget/tests/main.nf.test index d7eb12b7dba..925e21375d7 100644 --- a/modules/nf-core/nextclade/datasetget/tests/main.nf.test +++ b/modules/nf-core/nextclade/datasetget/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = 'nextstrain/sars-cov-2/wuhan-hu-1/orfs' input[1] = '2024-01-16--20-31-02Z' @@ -35,6 +36,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = 'nextstrain/sars-cov-2/wuhan-hu-1/orfs' input[1] = '2024-01-16--20-31-02Z' diff --git a/modules/nf-core/nextclade/run/tests/main.nf.test b/modules/nf-core/nextclade/run/tests/main.nf.test index b486a3fe6b8..f614c3db0f3 100644 --- a/modules/nf-core/nextclade/run/tests/main.nf.test +++ b/modules/nf-core/nextclade/run/tests/main.nf.test @@ -29,6 +29,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [[id: 'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] @@ -63,6 +64,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [[id: 'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] diff --git a/modules/nf-core/nextgenmap/tests/main.nf.test b/modules/nf-core/nextgenmap/tests/main.nf.test index c18a3d130df..5c5fb99f637 100644 --- a/modules/nf-core/nextgenmap/tests/main.nf.test +++ b/modules/nf-core/nextgenmap/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map [ @@ -43,6 +44,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ @@ -74,6 +76,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ diff --git a/modules/nf-core/ngmaster/tests/main.nf.test b/modules/nf-core/ngmaster/tests/main.nf.test index f30ca72aa2f..1b95ef3a426 100644 --- a/modules/nf-core/ngmaster/tests/main.nf.test +++ b/modules/nf-core/ngmaster/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] @@ -35,6 +36,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] diff --git a/modules/nf-core/ngmerge/tests/main.nf.test b/modules/nf-core/ngmerge/tests/main.nf.test index 826db1b8ddb..93dac48e48a 100644 --- a/modules/nf-core/ngmerge/tests/main.nf.test +++ b/modules/nf-core/ngmerge/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ diff --git a/modules/nf-core/ngsbits/samplegender/tests/main.nf.test b/modules/nf-core/ngsbits/samplegender/tests/main.nf.test index 4f8379b4022..c70d7dc70a9 100644 --- a/modules/nf-core/ngsbits/samplegender/tests/main.nf.test +++ b/modules/nf-core/ngsbits/samplegender/tests/main.nf.test @@ -17,6 +17,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), diff --git a/modules/nf-core/ngscheckmate/fastq/tests/main.nf.test b/modules/nf-core/ngscheckmate/fastq/tests/main.nf.test index 287aed75681..a5df5f10ccc 100644 --- a/modules/nf-core/ngscheckmate/fastq/tests/main.nf.test +++ b/modules/nf-core/ngscheckmate/fastq/tests/main.nf.test @@ -81,6 +81,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test_paired', single_end:false ], // meta map [ @@ -109,6 +110,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test_paired', single_end:false ], // meta map [ diff --git a/modules/nf-core/ngscheckmate/ncm/tests/main.nf.test b/modules/nf-core/ngscheckmate/ncm/tests/main.nf.test index 1263be3583f..bc46317c1b4 100644 --- a/modules/nf-core/ngscheckmate/ncm/tests/main.nf.test +++ b/modules/nf-core/ngscheckmate/ncm/tests/main.nf.test @@ -67,6 +67,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id: 'combined_bams' ], [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), @@ -102,6 +103,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = BCFTOOLS_MPILEUP1.out.vcf.combine(BCFTOOLS_MPILEUP2.out.vcf.map{it[1]}).map{meta, one, two -> [meta, [one, two]]}.map{meta, stuff -> [meta, stuff.flatten()]} input[1] = BEDTOOLS_MAKEWINDOWS.out.bed input[2] = [ [ id:'sarscov2' ], @@ -133,6 +135,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id: 'combined_bams' ], [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), @@ -165,6 +168,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = BCFTOOLS_MPILEUP1.out.vcf.combine(BCFTOOLS_MPILEUP2.out.vcf.map{it[1]}) input[1] = BEDTOOLS_MAKEWINDOWS.out.bed input[2] = [ [ id:'sarscov2' ], diff --git a/modules/nf-core/ngscheckmate/patterngenerator/tests/main.nf.test b/modules/nf-core/ngscheckmate/patterngenerator/tests/main.nf.test index cc5fc0d20be..c72f046f769 100644 --- a/modules/nf-core/ngscheckmate/patterngenerator/tests/main.nf.test +++ b/modules/nf-core/ngscheckmate/patterngenerator/tests/main.nf.test @@ -31,6 +31,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) @@ -62,6 +63,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) diff --git a/modules/nf-core/ngscheckmate/vafncm/tests/main.nf.test b/modules/nf-core/ngscheckmate/vafncm/tests/main.nf.test index d90e8f0c66d..5a120f06538 100644 --- a/modules/nf-core/ngscheckmate/vafncm/tests/main.nf.test +++ b/modules/nf-core/ngscheckmate/vafncm/tests/main.nf.test @@ -116,6 +116,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = NGSCHECKMATE_FASTQ.out.vaf.map{it[1]}.collect().map{files -> [[id:"combined"], files]} """ } @@ -141,6 +142,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = NGSCHECKMATE_FASTQ.out.vaf.map{it[1]}.collect().map{files -> [[id:"combined"], files]} """ } diff --git a/modules/nf-core/nonpareil/curve/tests/main.nf.test b/modules/nf-core/nonpareil/curve/tests/main.nf.test index ee6a16d53a2..737b18de6b0 100644 --- a/modules/nf-core/nonpareil/curve/tests/main.nf.test +++ b/modules/nf-core/nonpareil/curve/tests/main.nf.test @@ -31,6 +31,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = NONPAREIL_NONPAREIL.out.npo """ } diff --git a/modules/nf-core/nonpareil/nonpareil/tests/main.nf.test b/modules/nf-core/nonpareil/nonpareil/tests/main.nf.test index be4e2b3fa2b..1a803d899b0 100644 --- a/modules/nf-core/nonpareil/nonpareil/tests/main.nf.test +++ b/modules/nf-core/nonpareil/nonpareil/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/prokaryotes/candidatus_portiera_aleyrodidarum/illumina/fastq/test_1.fastq.gz', checkIfExists: true) @@ -61,6 +62,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = GUNZIP.out.gunzip input[1] = 'fastq' input[2] = 'kmer' @@ -91,6 +93,7 @@ test("candidatus_portiera_aleyrodidarum - stub") { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/prokaryotes/candidatus_portiera_aleyrodidarum/illumina/fastq/test_1.fastq.gz', checkIfExists: true) diff --git a/modules/nf-core/nonpareil/nonpareilcurvesr/tests/main.nf.test b/modules/nf-core/nonpareil/nonpareilcurvesr/tests/main.nf.test index 9542020735d..de52ec2ff8c 100644 --- a/modules/nf-core/nonpareil/nonpareilcurvesr/tests/main.nf.test +++ b/modules/nf-core/nonpareil/nonpareilcurvesr/tests/main.nf.test @@ -31,6 +31,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = NONPAREIL_NONPAREIL.out.npo.map{meta, npo -> [[id:'test'], npo]}.groupTuple() """ } @@ -59,6 +60,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = NONPAREIL_NONPAREIL.out.npo.map{meta, npo -> [[id:'test'], npo]}.groupTuple() """ } diff --git a/modules/nf-core/nonpareil/set/tests/main.nf.test b/modules/nf-core/nonpareil/set/tests/main.nf.test index 23e7fa97230..ee4d00a79a6 100644 --- a/modules/nf-core/nonpareil/set/tests/main.nf.test +++ b/modules/nf-core/nonpareil/set/tests/main.nf.test @@ -31,6 +31,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = NONPAREIL_NONPAREIL.out.npo.map{meta, npo -> [[id:'test'], npo]}.groupTuple() """ } @@ -56,6 +57,7 @@ test("candidatus_portiera_aleyrodidarum - stub") { when { process { """ + // testy mctestface input[0] = NONPAREIL_NONPAREIL.out.npo.map{meta, npo -> [[id:'test'], npo]}.groupTuple() """ } diff --git a/modules/nf-core/odgi/build/tests/main.nf.test b/modules/nf-core/odgi/build/tests/main.nf.test index d2f6a5f5813..489ae93b8f1 100644 --- a/modules/nf-core/odgi/build/tests/main.nf.test +++ b/modules/nf-core/odgi/build/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'pangenomics/homo_sapiens/pangenome.smoothxg.gfa', checkIfExists: true) diff --git a/modules/nf-core/odgi/draw/tests/main.nf.test b/modules/nf-core/odgi/draw/tests/main.nf.test index 8b59a7f80ab..db066b58311 100644 --- a/modules/nf-core/odgi/draw/tests/main.nf.test +++ b/modules/nf-core/odgi/draw/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'pangenomics/homo_sapiens/odgi/pangenome.og', checkIfExists: true), diff --git a/modules/nf-core/odgi/layout/tests/main.nf.test b/modules/nf-core/odgi/layout/tests/main.nf.test index f8daf7034c0..3c8f7956fce 100644 --- a/modules/nf-core/odgi/layout/tests/main.nf.test +++ b/modules/nf-core/odgi/layout/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'pangenomics/homo_sapiens/pangenome.smoothxg.gfa', checkIfExists: true) diff --git a/modules/nf-core/odgi/sort/tests/main.nf.test b/modules/nf-core/odgi/sort/tests/main.nf.test index e9bb390b883..5e38642416a 100644 --- a/modules/nf-core/odgi/sort/tests/main.nf.test +++ b/modules/nf-core/odgi/sort/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'pangenomics/homo_sapiens/pangenome.smoothxg.gfa', checkIfExists: true) diff --git a/modules/nf-core/odgi/squeeze/tests/main.nf.test b/modules/nf-core/odgi/squeeze/tests/main.nf.test index a5d35948cf9..b6ad819a381 100644 --- a/modules/nf-core/odgi/squeeze/tests/main.nf.test +++ b/modules/nf-core/odgi/squeeze/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'pangenomics/homo_sapiens/odgi/pangenome.og', checkIfExists: true) diff --git a/modules/nf-core/odgi/stats/tests/main.nf.test b/modules/nf-core/odgi/stats/tests/main.nf.test index b0cc80d26fb..6f627500106 100644 --- a/modules/nf-core/odgi/stats/tests/main.nf.test +++ b/modules/nf-core/odgi/stats/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'pangenomics/homo_sapiens/pangenome.smoothxg.gfa', checkIfExists: true) diff --git a/modules/nf-core/odgi/unchop/tests/main.nf.test b/modules/nf-core/odgi/unchop/tests/main.nf.test index 3096e135d24..2a7e1ec03bc 100644 --- a/modules/nf-core/odgi/unchop/tests/main.nf.test +++ b/modules/nf-core/odgi/unchop/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'pangenomics/homo_sapiens/pangenome.smoothxg.gfa', checkIfExists: true) diff --git a/modules/nf-core/odgi/view/tests/main.nf.test b/modules/nf-core/odgi/view/tests/main.nf.test index 788f3c44371..34a6e84d40f 100644 --- a/modules/nf-core/odgi/view/tests/main.nf.test +++ b/modules/nf-core/odgi/view/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'pangenomics/homo_sapiens/pangenome.smoothxg.gfa', checkIfExists: true) diff --git a/modules/nf-core/odgi/viz/tests/main.nf.test b/modules/nf-core/odgi/viz/tests/main.nf.test index a4d89049af3..e11669ad142 100644 --- a/modules/nf-core/odgi/viz/tests/main.nf.test +++ b/modules/nf-core/odgi/viz/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'pangenomics/homo_sapiens/pangenome.smoothxg.gfa', checkIfExists: true) diff --git a/modules/nf-core/openms/decoydatabase/tests/main.nf.test b/modules/nf-core/openms/decoydatabase/tests/main.nf.test index d0d5db211ea..f3943694962 100644 --- a/modules/nf-core/openms/decoydatabase/tests/main.nf.test +++ b/modules/nf-core/openms/decoydatabase/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id:'test'], file(params.modules_testdata_base_path + 'proteomics/database/yeast_UPS.fasta', checkIfExists: true) diff --git a/modules/nf-core/openms/idfilter/tests/main.nf.test b/modules/nf-core/openms/idfilter/tests/main.nf.test index ec98829fad1..d9add581c25 100644 --- a/modules/nf-core/openms/idfilter/tests/main.nf.test +++ b/modules/nf-core/openms/idfilter/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], // meta map file(params.modules_testdata_base_path +'/proteomics/openms/HepG2_rep1_small.idXML', checkIfExists: true), @@ -38,6 +39,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], // meta map file(params.modules_testdata_base_path +'/proteomics/openms/HepG2_rep1_small.idXML', checkIfExists: true), diff --git a/modules/nf-core/openms/idmassaccuracy/tests/main.nf.test b/modules/nf-core/openms/idmassaccuracy/tests/main.nf.test index b267fe15623..1fb44dc25ae 100644 --- a/modules/nf-core/openms/idmassaccuracy/tests/main.nf.test +++ b/modules/nf-core/openms/idmassaccuracy/tests/main.nf.test @@ -50,6 +50,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = THERMORAWFILEPARSER.out.spectra.join(OPENMSTHIRDPARTY_COMETADAPTER.out.idxml) """ } @@ -67,6 +68,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = THERMORAWFILEPARSER.out.spectra.join(OPENMSTHIRDPARTY_COMETADAPTER.out.idxml) """ } diff --git a/modules/nf-core/openms/idmerger/tests/main.nf.test b/modules/nf-core/openms/idmerger/tests/main.nf.test index 8945e0914eb..00055a1c82d 100644 --- a/modules/nf-core/openms/idmerger/tests/main.nf.test +++ b/modules/nf-core/openms/idmerger/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test'], // meta map [ file(params.modules_testdata_base_path + 'proteomics/openms/HepG2_rep1_small.idXML', checkIfExists: true), @@ -45,6 +46,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test'], // meta map [ file(params.modules_testdata_base_path + 'proteomics/openms/HepG2_rep1_small.idXML', checkIfExists: true), diff --git a/modules/nf-core/openms/idripper/tests/main.nf.test b/modules/nf-core/openms/idripper/tests/main.nf.test index 1e9b40d7aaa..e0039519b1d 100644 --- a/modules/nf-core/openms/idripper/tests/main.nf.test +++ b/modules/nf-core/openms/idripper/tests/main.nf.test @@ -34,6 +34,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = OPENMS_IDMERGER.out.idxml """ } @@ -55,6 +56,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = OPENMS_IDMERGER.out.idxml """ } diff --git a/modules/nf-core/openms/idscoreswitcher/tests/main.nf.test b/modules/nf-core/openms/idscoreswitcher/tests/main.nf.test index 561f832096f..d6b08decbdc 100644 --- a/modules/nf-core/openms/idscoreswitcher/tests/main.nf.test +++ b/modules/nf-core/openms/idscoreswitcher/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id:'test'], file(params.modules_testdata_base_path + 'proteomics/openms/HepG2_rep1_small.idXML', checkIfExists: true) @@ -39,6 +40,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id:'test'], file(params.modules_testdata_base_path + 'proteomics/openms/HepG2_rep1_small.idXML', checkIfExists: true) diff --git a/modules/nf-core/openms/peakpickerhires/tests/main.nf.test b/modules/nf-core/openms/peakpickerhires/tests/main.nf.test index df2071c4d7b..5bee18e6a98 100644 --- a/modules/nf-core/openms/peakpickerhires/tests/main.nf.test +++ b/modules/nf-core/openms/peakpickerhires/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], // meta map file(params.modules_testdata_base_path + 'proteomics/msspectra/peakpicker_tutorial_1.mzML', checkIfExists: true) @@ -39,6 +40,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test_stub'], // meta map file(params.modules_testdata_base_path + 'proteomics/msspectra/peakpicker_tutorial_1.mzML', checkIfExists: true) diff --git a/modules/nf-core/openms/peptideindexer/tests/main.nf.test b/modules/nf-core/openms/peptideindexer/tests/main.nf.test index 1238bc361de..b6ed7cb4819 100644 --- a/modules/nf-core/openms/peptideindexer/tests/main.nf.test +++ b/modules/nf-core/openms/peptideindexer/tests/main.nf.test @@ -30,6 +30,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id:'test'], file(params.modules_testdata_base_path + 'proteomics/openms/HepG2_rep1_small.idXML', checkIfExists: true) @@ -56,6 +57,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id:'test'], file(params.modules_testdata_base_path + 'proteomics/openms/HepG2_rep1_small.idXML', checkIfExists: true) diff --git a/modules/nf-core/openmsthirdparty/cometadapter/tests/main.nf.test b/modules/nf-core/openmsthirdparty/cometadapter/tests/main.nf.test index cf1a0bcddcd..f35fd588838 100644 --- a/modules/nf-core/openmsthirdparty/cometadapter/tests/main.nf.test +++ b/modules/nf-core/openmsthirdparty/cometadapter/tests/main.nf.test @@ -44,6 +44,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = THERMORAWFILEPARSER.out.spectra.join( OPENMS_DECOYDATABASE.out.decoy_fasta @@ -70,6 +71,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = THERMORAWFILEPARSER.out.spectra.join( OPENMS_DECOYDATABASE.out.decoy_fasta diff --git a/modules/nf-core/optitype/tests/main.nf.test b/modules/nf-core/optitype/tests/main.nf.test index 3a6206c8192..5a6152332ff 100644 --- a/modules/nf-core/optitype/tests/main.nf.test +++ b/modules/nf-core/optitype/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', seq_type:'dna' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/example_hla_pe.sorted.bam', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/example_hla_pe.sorted.bam.bai', checkIfExists: true) @@ -41,6 +42,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', seq_type:'dna' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/example_hla_pe.sorted.bam', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/example_hla_pe.sorted.bam.bai', checkIfExists: true) diff --git a/modules/nf-core/orthofinder/tests/main.nf.test b/modules/nf-core/orthofinder/tests/main.nf.test index aa68d1d21ab..a6547ca2cde 100644 --- a/modules/nf-core/orthofinder/tests/main.nf.test +++ b/modules/nf-core/orthofinder/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/proteome.fasta', checkIfExists: true) .copyTo("${workDir}/sarscov2.fasta") @@ -82,6 +83,7 @@ nextflow_process { when { process { """ + // testy mctestface file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/proteome.fasta', checkIfExists: true) .copyTo("${workDir}/sarscov2.fasta") @@ -128,6 +130,7 @@ nextflow_process { when { process { """ + // testy mctestface file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/proteome.fasta', checkIfExists: true) .copyTo("${workDir}/sarscov2.fasta") diff --git a/modules/nf-core/paftools/sam2paf/tests/main.nf.test b/modules/nf-core/paftools/sam2paf/tests/main.nf.test index be31cc33c4f..ed57ccbc5e3 100644 --- a/modules/nf-core/paftools/sam2paf/tests/main.nf.test +++ b/modules/nf-core/paftools/sam2paf/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id:'test'], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/scramble/test.bam', checkIfExists: true) @@ -37,6 +38,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id:'test'], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/scramble/test.bam', checkIfExists: true) diff --git a/modules/nf-core/pairix/tests/main.nf.test b/modules/nf-core/pairix/tests/main.nf.test index bcfffff8549..506ebc473fe 100644 --- a/modules/nf-core/pairix/tests/main.nf.test +++ b/modules/nf-core/pairix/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file("https://raw.githubusercontent.com/4dn-dcic/pairix/master/samples/4dn.bsorted.chr21_22_only.nontriangle.pairs.gz", checkIfExists: true) ] diff --git a/modules/nf-core/pairtools/dedup/tests/main.nf.test b/modules/nf-core/pairtools/dedup/tests/main.nf.test index 41bbfabb45c..41204a6deee 100644 --- a/modules/nf-core/pairtools/dedup/tests/main.nf.test +++ b/modules/nf-core/pairtools/dedup/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pairtools/mock.4dedup.pairsam', checkIfExists: true) ] diff --git a/modules/nf-core/pairtools/flip/tests/main.nf.test b/modules/nf-core/pairtools/flip/tests/main.nf.test index e94ffe55455..c660c78df69 100644 --- a/modules/nf-core/pairtools/flip/tests/main.nf.test +++ b/modules/nf-core/pairtools/flip/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pairtools/mock.4flip.pairs', checkIfExists: true) ] input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pairtools/mock.chrom.sizes', checkIfExists: true) diff --git a/modules/nf-core/pairtools/merge/tests/main.nf.test b/modules/nf-core/pairtools/merge/tests/main.nf.test index d9cfa7d034a..1c3b0e5d3bc 100644 --- a/modules/nf-core/pairtools/merge/tests/main.nf.test +++ b/modules/nf-core/pairtools/merge/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pairtools/mock.pairsam', checkIfExists: true) ] diff --git a/modules/nf-core/pairtools/parse/tests/main.nf.test b/modules/nf-core/pairtools/parse/tests/main.nf.test index 27f9bc32599..9954682c802 100644 --- a/modules/nf-core/pairtools/parse/tests/main.nf.test +++ b/modules/nf-core/pairtools/parse/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pairtools/mock.sam', checkIfExists: true) ] input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pairtools/mock.chrom.sizes', checkIfExists: true) diff --git a/modules/nf-core/pairtools/restrict/tests/main.nf.test b/modules/nf-core/pairtools/restrict/tests/main.nf.test index b9fa5c8723c..ef12d9f034f 100644 --- a/modules/nf-core/pairtools/restrict/tests/main.nf.test +++ b/modules/nf-core/pairtools/restrict/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pairtools/mock.4flip.pairs', checkIfExists: true) ] diff --git a/modules/nf-core/pairtools/select/tests/main.nf.test b/modules/nf-core/pairtools/select/tests/main.nf.test index ec4ece4f71f..c03a38ef972 100644 --- a/modules/nf-core/pairtools/select/tests/main.nf.test +++ b/modules/nf-core/pairtools/select/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pairtools/mock.pairsam', checkIfExists: true) ] diff --git a/modules/nf-core/pairtools/sort/tests/main.nf.test b/modules/nf-core/pairtools/sort/tests/main.nf.test index a4e789bc58d..d346cf36bea 100644 --- a/modules/nf-core/pairtools/sort/tests/main.nf.test +++ b/modules/nf-core/pairtools/sort/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pairtools/mock.pairsam', checkIfExists: true) ] diff --git a/modules/nf-core/pairtools/split/tests/main.nf.test b/modules/nf-core/pairtools/split/tests/main.nf.test index ad050dec984..34d3c50f0e8 100644 --- a/modules/nf-core/pairtools/split/tests/main.nf.test +++ b/modules/nf-core/pairtools/split/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pairtools/mock.pairsam', checkIfExists: true) ] @@ -39,6 +40,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pairtools/mock.pairsam', checkIfExists: true) ] diff --git a/modules/nf-core/pairtools/stats/tests/main.nf.test b/modules/nf-core/pairtools/stats/tests/main.nf.test index 3e66596177c..f22da512b84 100644 --- a/modules/nf-core/pairtools/stats/tests/main.nf.test +++ b/modules/nf-core/pairtools/stats/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pairtools/mock.pairsam', checkIfExists: true) ] diff --git a/modules/nf-core/panacus/histgrowth/tests/main.nf.test b/modules/nf-core/panacus/histgrowth/tests/main.nf.test index d6809c4c91d..701ff8c9436 100644 --- a/modules/nf-core/panacus/histgrowth/tests/main.nf.test +++ b/modules/nf-core/panacus/histgrowth/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'pangenomics/homo_sapiens/pangenome.smoothxg.gfa', checkIfExists: true) diff --git a/modules/nf-core/panacus/visualize/tests/main.nf.test b/modules/nf-core/panacus/visualize/tests/main.nf.test index 96f96c9dde0..ef6102b7aca 100644 --- a/modules/nf-core/panacus/visualize/tests/main.nf.test +++ b/modules/nf-core/panacus/visualize/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'pangenomics/homo_sapiens/pangenome.panacus.tsv', checkIfExists: true) diff --git a/modules/nf-core/panaroo/run/tests/main.nf.test b/modules/nf-core/panaroo/run/tests/main.nf.test index d1a6784e939..f9b909aff22 100644 --- a/modules/nf-core/panaroo/run/tests/main.nf.test +++ b/modules/nf-core/panaroo/run/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ diff --git a/modules/nf-core/paragraph/vcf2paragraph/tests/main.nf.test b/modules/nf-core/paragraph/vcf2paragraph/tests/main.nf.test index 16741305401..9d39aed7931 100644 --- a/modules/nf-core/paragraph/vcf2paragraph/tests/main.nf.test +++ b/modules/nf-core/paragraph/vcf2paragraph/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz', checkIfExists: true) @@ -43,6 +44,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz', checkIfExists: true) diff --git a/modules/nf-core/paraphase/tests/main.nf.test b/modules/nf-core/paraphase/tests/main.nf.test index e34d6699147..ce236ddca84 100644 --- a/modules/nf-core/paraphase/tests/main.nf.test +++ b/modules/nf-core/paraphase/tests/main.nf.test @@ -30,6 +30,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/test.sorted.bam', checkIfExists: true), @@ -69,6 +70,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/test.sorted.bam', checkIfExists: true), @@ -107,6 +109,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/test.sorted.bam', checkIfExists: true), @@ -146,6 +149,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/test.sorted.bam', checkIfExists: true), @@ -176,6 +180,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/test.sorted.bam', checkIfExists: true), @@ -206,6 +211,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/test.sorted.bam', checkIfExists: true), diff --git a/modules/nf-core/pasty/tests/main.nf.test b/modules/nf-core/pasty/tests/main.nf.test index b741f14e987..955c0f2a822 100644 --- a/modules/nf-core/pasty/tests/main.nf.test +++ b/modules/nf-core/pasty/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] @@ -36,6 +37,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] diff --git a/modules/nf-core/pbbam/pbmerge/tests/main.nf.test b/modules/nf-core/pbbam/pbmerge/tests/main.nf.test index 303d30f879a..2d001dbb0ff 100644 --- a/modules/nf-core/pbbam/pbmerge/tests/main.nf.test +++ b/modules/nf-core/pbbam/pbmerge/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ @@ -48,6 +49,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ diff --git a/modules/nf-core/pbccs/tests/main.nf.test b/modules/nf-core/pbccs/tests/main.nf.test index ef70d05833b..e53b7422718 100644 --- a/modules/nf-core/pbccs/tests/main.nf.test +++ b/modules/nf-core/pbccs/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'alz' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/alz.bam', checkIfExists: true), @@ -46,6 +47,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'alz' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/alz.bam', checkIfExists: true), diff --git a/modules/nf-core/pbptyper/tests/main.nf.test b/modules/nf-core/pbptyper/tests/main.nf.test index 3f6146e6f40..76e3bbeb55e 100644 --- a/modules/nf-core/pbptyper/tests/main.nf.test +++ b/modules/nf-core/pbptyper/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) @@ -38,6 +39,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) diff --git a/modules/nf-core/pbtk/bam2fastq/tests/main.nf.test b/modules/nf-core/pbtk/bam2fastq/tests/main.nf.test index bd093078d33..2645fea2e1e 100644 --- a/modules/nf-core/pbtk/bam2fastq/tests/main.nf.test +++ b/modules/nf-core/pbtk/bam2fastq/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/alz.bam', checkIfExists: true), @@ -39,6 +40,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/alz.bam', checkIfExists: true), @@ -64,6 +66,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/alz.bam', checkIfExists: true), @@ -90,6 +93,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/alz.bam', checkIfExists: true), diff --git a/modules/nf-core/pbtk/pbindex/tests/main.nf.test b/modules/nf-core/pbtk/pbindex/tests/main.nf.test index d2e420bfe0d..4acb82e7ea6 100644 --- a/modules/nf-core/pbtk/pbindex/tests/main.nf.test +++ b/modules/nf-core/pbtk/pbindex/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/alz.bam', checkIfExists: true) @@ -38,6 +39,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/alz.bam', checkIfExists: true) diff --git a/modules/nf-core/pear/tests/main.nf.test b/modules/nf-core/pear/tests/main.nf.test index 31173d1cc10..2e7beffa54b 100644 --- a/modules/nf-core/pear/tests/main.nf.test +++ b/modules/nf-core/pear/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ diff --git a/modules/nf-core/peddy/tests/main.nf.test b/modules/nf-core/peddy/tests/main.nf.test index 21ff538d16b..068c9869faa 100644 --- a/modules/nf-core/peddy/tests/main.nf.test +++ b/modules/nf-core/peddy/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/ped/justhusky_minimal.vcf.gz', checkIfExists: true), diff --git a/modules/nf-core/peka/tests/main.nf.test b/modules/nf-core/peka/tests/main.nf.test index dc0dd034359..3e87358a22e 100644 --- a/modules/nf-core/peka/tests/main.nf.test +++ b/modules/nf-core/peka/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file("https://raw.githubusercontent.com/nf-core/test-datasets/clipseq/peka/chr21_HepG2-PCBP1-merged.xl10_200_density2_peaks.bed", checkIfExists: true) ] input[1] = [ [ id:'test' ], file("https://raw.githubusercontent.com/nf-core/test-datasets/clipseq/peka/chr21_HepG2-PCBP1-merged.xl.bed", checkIfExists: true) ] input[2] = file("https://raw.githubusercontent.com/nf-core/test-datasets/clipseq/peka/chr21.GRCh38.p12.genome.masked.fa", checkIfExists: true) @@ -44,6 +45,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file("https://raw.githubusercontent.com/nf-core/test-datasets/clipseq/peka/chr21_HepG2-PCBP1-merged.xl10_200_density2_peaks.bed", checkIfExists: true) ] input[1] = [ [ id:'test' ], file("https://raw.githubusercontent.com/nf-core/test-datasets/clipseq/peka/chr21_HepG2-PCBP1-merged.xl.bed", checkIfExists: true) ] input[2] = file("https://raw.githubusercontent.com/nf-core/test-datasets/clipseq/peka/chr21.GRCh38.p12.genome.masked.fa", checkIfExists: true) diff --git a/modules/nf-core/phantompeakqualtools/tests/main.nf.test b/modules/nf-core/phantompeakqualtools/tests/main.nf.test index ea096bcfb95..ec7bb4760bd 100644 --- a/modules/nf-core/phantompeakqualtools/tests/main.nf.test +++ b/modules/nf-core/phantompeakqualtools/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.bam', checkIfExists: true) @@ -41,6 +42,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) @@ -70,6 +72,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) diff --git a/modules/nf-core/pharokka/pharokka/tests/main.nf.test b/modules/nf-core/pharokka/pharokka/tests/main.nf.test index 9d89dc196e5..2a16aba8fdc 100644 --- a/modules/nf-core/pharokka/pharokka/tests/main.nf.test +++ b/modules/nf-core/pharokka/pharokka/tests/main.nf.test @@ -21,6 +21,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) diff --git a/modules/nf-core/phispy/tests/main.nf.test b/modules/nf-core/phispy/tests/main.nf.test index 4672848432e..fc3bc7c3124 100644 --- a/modules/nf-core/phispy/tests/main.nf.test +++ b/modules/nf-core/phispy/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file( params.modules_testdata_base_path + "/genomics/prokaryotes/bacteroides_fragilis/genome/genome.gbff.gz", checkIfExists: true ) @@ -53,6 +54,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file( params.modules_testdata_base_path + "/genomics/prokaryotes/bacteroides_fragilis/genome/genome.gbff.gz", checkIfExists: true ) diff --git a/modules/nf-core/picard/addorreplacereadgroups/tests/main.nf.test b/modules/nf-core/picard/addorreplacereadgroups/tests/main.nf.test index 9c029354f15..9810df4469c 100644 --- a/modules/nf-core/picard/addorreplacereadgroups/tests/main.nf.test +++ b/modules/nf-core/picard/addorreplacereadgroups/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [:], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) ] input[1] = [ [:], [] ] input[2] = [ [:], [] ] @@ -43,6 +44,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ @@ -74,6 +76,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [:], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) ] input[1] = [ [:], [] ] input[2] = [ [:], [] ] diff --git a/modules/nf-core/picard/bedtointervallist/tests/main.nf.test b/modules/nf-core/picard/bedtointervallist/tests/main.nf.test index fd132089a41..0eef8f08584 100644 --- a/modules/nf-core/picard/bedtointervallist/tests/main.nf.test +++ b/modules/nf-core/picard/bedtointervallist/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) ] diff --git a/modules/nf-core/picard/cleansam/tests/main.nf.test b/modules/nf-core/picard/cleansam/tests/main.nf.test index 5d80739a472..939c3dddc14 100644 --- a/modules/nf-core/picard/cleansam/tests/main.nf.test +++ b/modules/nf-core/picard/cleansam/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.bam', checkIfExists: true) diff --git a/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test b/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test index 3bbbd8cf5ca..309997633d1 100644 --- a/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test +++ b/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), @@ -53,6 +54,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), @@ -81,6 +83,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), @@ -118,6 +121,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), @@ -156,6 +160,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), diff --git a/modules/nf-core/picard/collectinsertsizemetrics/tests/main.nf.test b/modules/nf-core/picard/collectinsertsizemetrics/tests/main.nf.test index 4cf7a33236c..46b44eda39d 100644 --- a/modules/nf-core/picard/collectinsertsizemetrics/tests/main.nf.test +++ b/modules/nf-core/picard/collectinsertsizemetrics/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) @@ -42,6 +43,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) diff --git a/modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test b/modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test index 5b67774f720..fa5c1b1b1a8 100644 --- a/modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test +++ b/modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), @@ -48,6 +49,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), @@ -78,6 +80,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), diff --git a/modules/nf-core/picard/collectwgsmetrics/tests/main.nf.test b/modules/nf-core/picard/collectwgsmetrics/tests/main.nf.test index a3984566dcd..a4cadf35904 100644 --- a/modules/nf-core/picard/collectwgsmetrics/tests/main.nf.test +++ b/modules/nf-core/picard/collectwgsmetrics/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), @@ -50,6 +51,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), [] diff --git a/modules/nf-core/picard/createsequencedictionary/tests/main.nf.test b/modules/nf-core/picard/createsequencedictionary/tests/main.nf.test index 8152be96f31..7c6a7e225aa 100644 --- a/modules/nf-core/picard/createsequencedictionary/tests/main.nf.test +++ b/modules/nf-core/picard/createsequencedictionary/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)] @@ -42,6 +43,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)] diff --git a/modules/nf-core/picard/crosscheckfingerprints/tests/main.nf.test b/modules/nf-core/picard/crosscheckfingerprints/tests/main.nf.test index 33eb40de6fa..fba54416cf9 100644 --- a/modules/nf-core/picard/crosscheckfingerprints/tests/main.nf.test +++ b/modules/nf-core/picard/crosscheckfingerprints/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], //meta [ @@ -50,6 +51,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], //meta [ diff --git a/modules/nf-core/picard/fastqtosam/tests/main.nf.test b/modules/nf-core/picard/fastqtosam/tests/main.nf.test index ad3d52374a0..186b6df3b77 100644 --- a/modules/nf-core/picard/fastqtosam/tests/main.nf.test +++ b/modules/nf-core/picard/fastqtosam/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map [ @@ -43,6 +44,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ @@ -73,6 +75,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ diff --git a/modules/nf-core/picard/fixmateinformation/tests/main.nf.test b/modules/nf-core/picard/fixmateinformation/tests/main.nf.test index b45bdde582d..b1b7311ead4 100644 --- a/modules/nf-core/picard/fixmateinformation/tests/main.nf.test +++ b/modules/nf-core/picard/fixmateinformation/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) diff --git a/modules/nf-core/picard/liftovervcf/tests/main.nf.test b/modules/nf-core/picard/liftovervcf/tests/main.nf.test index 7b42102dec5..10d06482e14 100644 --- a/modules/nf-core/picard/liftovervcf/tests/main.nf.test +++ b/modules/nf-core/picard/liftovervcf/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf', checkIfExists: true) ] @@ -51,6 +52,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf', checkIfExists: true) ] diff --git a/modules/nf-core/picard/markduplicates/tests/main.nf.test b/modules/nf-core/picard/markduplicates/tests/main.nf.test index 9ed90965929..71722140757 100644 --- a/modules/nf-core/picard/markduplicates/tests/main.nf.test +++ b/modules/nf-core/picard/markduplicates/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) @@ -41,6 +42,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) @@ -68,6 +70,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true) @@ -101,6 +104,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) @@ -124,6 +128,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) @@ -147,6 +152,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true) diff --git a/modules/nf-core/picard/mergesamfiles/tests/main.nf.test b/modules/nf-core/picard/mergesamfiles/tests/main.nf.test index 7b45f051a43..33969b05c19 100644 --- a/modules/nf-core/picard/mergesamfiles/tests/main.nf.test +++ b/modules/nf-core/picard/mergesamfiles/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.bam', checkIfExists: true), ] diff --git a/modules/nf-core/picard/positionbaseddownsamplesam/tests/main.nf.test b/modules/nf-core/picard/positionbaseddownsamplesam/tests/main.nf.test index 64dcdbcc189..e243edd6000 100644 --- a/modules/nf-core/picard/positionbaseddownsamplesam/tests/main.nf.test +++ b/modules/nf-core/picard/positionbaseddownsamplesam/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), @@ -42,6 +43,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), diff --git a/modules/nf-core/picard/renamesampleinvcf/tests/main.nf.test b/modules/nf-core/picard/renamesampleinvcf/tests/main.nf.test index f755447ff4c..67375f86cb7 100644 --- a/modules/nf-core/picard/renamesampleinvcf/tests/main.nf.test +++ b/modules/nf-core/picard/renamesampleinvcf/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf', checkIfExists: true) ] diff --git a/modules/nf-core/picard/scatterintervalsbyns/tests/main.nf.test b/modules/nf-core/picard/scatterintervalsbyns/tests/main.nf.test index 9b60ba023f8..abe9f49e7ea 100644 --- a/modules/nf-core/picard/scatterintervalsbyns/tests/main.nf.test +++ b/modules/nf-core/picard/scatterintervalsbyns/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) @@ -46,6 +47,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) diff --git a/modules/nf-core/picard/sortsam/tests/main.nf.test b/modules/nf-core/picard/sortsam/tests/main.nf.test index 9d9af09ea77..85c2e4ebd30 100644 --- a/modules/nf-core/picard/sortsam/tests/main.nf.test +++ b/modules/nf-core/picard/sortsam/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.bam', checkIfExists: true) ] diff --git a/modules/nf-core/picard/sortvcf/tests/main.nf.test b/modules/nf-core/picard/sortvcf/tests/main.nf.test index 9df73ad430f..ee0c42447cb 100644 --- a/modules/nf-core/picard/sortvcf/tests/main.nf.test +++ b/modules/nf-core/picard/sortvcf/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) ] diff --git a/modules/nf-core/pigz/compress/tests/main.nf.test b/modules/nf-core/pigz/compress/tests/main.nf.test index b3cb25e3667..d25ad27f5dd 100644 --- a/modules/nf-core/pigz/compress/tests/main.nf.test +++ b/modules/nf-core/pigz/compress/tests/main.nf.test @@ -12,6 +12,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) @@ -32,6 +33,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) diff --git a/modules/nf-core/pilon/tests/main.nf.test b/modules/nf-core/pilon/tests/main.nf.test index 2d09e8b85a6..d8fa69d47c0 100644 --- a/modules/nf-core/pilon/tests/main.nf.test +++ b/modules/nf-core/pilon/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true) ] @@ -40,6 +41,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true) ] @@ -66,6 +68,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true) ] @@ -92,6 +95,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true) ] diff --git a/modules/nf-core/pindel/pindel/tests/main.nf.test b/modules/nf-core/pindel/pindel/tests/main.nf.test index 4253407d2be..bf166df181b 100644 --- a/modules/nf-core/pindel/pindel/tests/main.nf.test +++ b/modules/nf-core/pindel/pindel/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false, insert_size:500 ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), diff --git a/modules/nf-core/pints/caller/tests/main.nf.test b/modules/nf-core/pints/caller/tests/main.nf.test index 0bb2a7cb1bf..052b1d8e95c 100644 --- a/modules/nf-core/pints/caller/tests/main.nf.test +++ b/modules/nf-core/pints/caller/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], [ @@ -48,6 +49,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file("https://raw.githubusercontent.com/Kraus-Lab/groHMM/master/inst/extdata/S0mR1.bam", checkIfExists: true), @@ -77,6 +79,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) diff --git a/modules/nf-core/pirate/tests/main.nf.test b/modules/nf-core/pirate/tests/main.nf.test index 7237b8acd9f..3ffe8c25168 100644 --- a/modules/nf-core/pirate/tests/main.nf.test +++ b/modules/nf-core/pirate/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ @@ -46,6 +47,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ diff --git a/modules/nf-core/plasmidfinder/tests/main.nf.test b/modules/nf-core/plasmidfinder/tests/main.nf.test index 1400d591084..fd696197916 100644 --- a/modules/nf-core/plasmidfinder/tests/main.nf.test +++ b/modules/nf-core/plasmidfinder/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) diff --git a/modules/nf-core/plasmidid/tests/main.nf.test b/modules/nf-core/plasmidid/tests/main.nf.test index 27e2a85dd54..42e18fb04d4 100644 --- a/modules/nf-core/plasmidid/tests/main.nf.test +++ b/modules/nf-core/plasmidid/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/contigs.fasta', checkIfExists: true) ] diff --git a/modules/nf-core/platypus/tests/main.nf.test b/modules/nf-core/platypus/tests/main.nf.test index e913ba3c6de..6386e3237c7 100644 --- a/modules/nf-core/platypus/tests/main.nf.test +++ b/modules/nf-core/platypus/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam.bai', checkIfExists: true), @@ -48,6 +49,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam.bai', checkIfExists: true), @@ -82,6 +84,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true), @@ -117,6 +120,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true), diff --git a/modules/nf-core/plink/bcf/tests/main.nf.test b/modules/nf-core/plink/bcf/tests/main.nf.test index 5db8bfb7143..9239ee32a1a 100644 --- a/modules/nf-core/plink/bcf/tests/main.nf.test +++ b/modules/nf-core/plink/bcf/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test_compressed_bcf', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.bcf', checkIfExists: true) diff --git a/modules/nf-core/plink/vcf/tests/main.nf.test b/modules/nf-core/plink/vcf/tests/main.nf.test index f091ac341fb..142c976f7f3 100644 --- a/modules/nf-core/plink/vcf/tests/main.nf.test +++ b/modules/nf-core/plink/vcf/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) ] @@ -38,6 +39,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) ] diff --git a/modules/nf-core/pmdtools/filter/tests/main.nf.test b/modules/nf-core/pmdtools/filter/tests/main.nf.test index d8fa6a13cf9..e1af04f8769 100644 --- a/modules/nf-core/pmdtools/filter/tests/main.nf.test +++ b/modules/nf-core/pmdtools/filter/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) ], @@ -46,6 +47,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) ], diff --git a/modules/nf-core/poolsnp/tests/main.nf.test b/modules/nf-core/poolsnp/tests/main.nf.test index 2130e272a02..bdde98715d3 100644 --- a/modules/nf-core/poolsnp/tests/main.nf.test +++ b/modules/nf-core/poolsnp/tests/main.nf.test @@ -31,6 +31,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = SAMTOOLS_MPILEUP.out.mpileup input[1] = Channel.of([ [ id:'test' ], // meta map @@ -63,6 +64,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = SAMTOOLS_MPILEUP.out.mpileup input[1] = Channel.of([ [ id:'test' ], // meta map @@ -95,6 +97,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = SAMTOOLS_MPILEUP.out.mpileup input[1] = Channel.of([ [ id:'test' ], // meta map @@ -129,6 +132,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = SAMTOOLS_MPILEUP.out.mpileup input[1] = Channel.of([ [ id:'test' ], // meta map diff --git a/modules/nf-core/popscle/demuxlet/tests/main.nf.test b/modules/nf-core/popscle/demuxlet/tests/main.nf.test index 7a12a0c2e00..6e8ca14dbf6 100644 --- a/modules/nf-core/popscle/demuxlet/tests/main.nf.test +++ b/modules/nf-core/popscle/demuxlet/tests/main.nf.test @@ -14,7 +14,8 @@ nextflow_process { test("demultiplexing - bam") { when { process { - """ + """ + // testy mctestface input[0] = [ [ id:'sample1'], [], @@ -54,6 +55,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = POPSCLE_DSCPILEUP.out.plp.collect{ meta, plp -> plp }.map{ plp -> [[ id: 'sample1'], plp[0].toString() - '.plp.gz', @@ -79,7 +81,8 @@ nextflow_process { when { process { - """ + """ + // testy mctestface input[0] = [ [ id:'sample1' ], [], diff --git a/modules/nf-core/popscle/dscpileup/tests/main.nf.test b/modules/nf-core/popscle/dscpileup/tests/main.nf.test index 7c3334b3ce8..1746cf5747d 100644 --- a/modules/nf-core/popscle/dscpileup/tests/main.nf.test +++ b/modules/nf-core/popscle/dscpileup/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'sample1' ], // meta map file(params.modules_testdata_base_path + '/genomics/homo_sapiens/demultiplexing/chr21.bam', checkIfExists: true), @@ -42,7 +43,8 @@ nextflow_process { when { process { - """ + """ + // testy mctestface input[0] = [ [ id:'sample1' ], // meta map file(params.modules_testdata_base_path + '/genomics/homo_sapiens/demultiplexing/chr21.bam', checkIfExists: true), diff --git a/modules/nf-core/popscle/freemuxlet/tests/main.nf.test b/modules/nf-core/popscle/freemuxlet/tests/main.nf.test index e8c2225c6e7..55e670c28e3 100644 --- a/modules/nf-core/popscle/freemuxlet/tests/main.nf.test +++ b/modules/nf-core/popscle/freemuxlet/tests/main.nf.test @@ -29,6 +29,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = POPSCLE_DSCPILEUP.out.plp.collect{ meta, plp -> plp }.map{ plp -> [[ id: 'sample1'], plp[0].getParent(), @@ -70,6 +71,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = POPSCLE_DSCPILEUP.out.plp.collect{ meta, plp -> plp }.map{ plp -> [[ id: 'sample1'], plp[0].getParent(), @@ -115,6 +117,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = POPSCLE_DSCPILEUP.out.plp.collect{ meta, plp -> plp }.map{ plp -> [[ id: 'sample1'], plp[0].toString() - '.plp.gz', @@ -158,6 +161,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = POPSCLE_DSCPILEUP.out.plp.collect{ meta, plp -> plp }.map{ plp -> [[ id: 'sample1'], plp[0].toString() - '.plp.gz', diff --git a/modules/nf-core/porechop/abi/tests/main.nf.test b/modules/nf-core/porechop/abi/tests/main.nf.test index b5a29f90846..ee550f5818a 100644 --- a/modules/nf-core/porechop/abi/tests/main.nf.test +++ b/modules/nf-core/porechop/abi/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/nanopore/fastq/test.fastq.gz', checkIfExists: true) diff --git a/modules/nf-core/porechop/porechop/tests/main.nf.test b/modules/nf-core/porechop/porechop/tests/main.nf.test index ed3f69865b0..56b605499e8 100644 --- a/modules/nf-core/porechop/porechop/tests/main.nf.test +++ b/modules/nf-core/porechop/porechop/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], file(params.modules_testdata_base_path + 'genomics/sarscov2/nanopore/fastq/test.fastq.gz', checkIfExists: true) @@ -42,6 +43,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], [] ] diff --git a/modules/nf-core/preseq/ccurve/tests/main.nf.test b/modules/nf-core/preseq/ccurve/tests/main.nf.test index 3c97d92cd67..325736fdf99 100644 --- a/modules/nf-core/preseq/ccurve/tests/main.nf.test +++ b/modules/nf-core/preseq/ccurve/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) @@ -42,6 +43,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) @@ -70,6 +72,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) diff --git a/modules/nf-core/preseq/lcextrap/tests/main.nf.test b/modules/nf-core/preseq/lcextrap/tests/main.nf.test index d1af1f0eddf..af976f9a684 100644 --- a/modules/nf-core/preseq/lcextrap/tests/main.nf.test +++ b/modules/nf-core/preseq/lcextrap/tests/main.nf.test @@ -12,6 +12,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:true ], // meta map [ file(params.modules_testdata_base_path + 'delete_me/preseq/SRR1003759_5M_subset.mr', checkIfExists: true) ] @@ -37,6 +38,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:true ], // meta map [ file(params.modules_testdata_base_path + 'delete_me/preseq/SRR1003759_5M_subset.mr', checkIfExists: true) ] @@ -57,6 +59,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map [ file(params.modules_testdata_base_path + 'delete_me/preseq/SRR1003759_5M_subset.mr', checkIfExists: true) ] @@ -82,6 +85,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map [ file(params.modules_testdata_base_path + 'delete_me/preseq/SRR1003759_5M_subset.mr', checkIfExists: true) ] diff --git a/modules/nf-core/president/tests/main.nf.test b/modules/nf-core/president/tests/main.nf.test index 13c7ebdb393..54d3d484ad3 100644 --- a/modules/nf-core/president/tests/main.nf.test +++ b/modules/nf-core/president/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id: "test" ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/all_sites.fas', checkIfExists: true) @@ -54,6 +55,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id: "test" ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/all_sites.fas', checkIfExists: true) @@ -93,6 +95,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id: "test" ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/all_sites.fas', checkIfExists: true) @@ -117,6 +120,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id: "test" ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/all_sites.fas', checkIfExists: true) diff --git a/modules/nf-core/presto/filterseq/tests/main.nf.test b/modules/nf-core/presto/filterseq/tests/main.nf.test index 62ced75c389..be2f3e0badb 100644 --- a/modules/nf-core/presto/filterseq/tests/main.nf.test +++ b/modules/nf-core/presto/filterseq/tests/main.nf.test @@ -31,6 +31,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = GUNZIP.out.gunzip """ } diff --git a/modules/nf-core/pretextmap/tests/main.nf.test b/modules/nf-core/pretextmap/tests/main.nf.test index cd2c3919a8b..748bb2996f8 100644 --- a/modules/nf-core/pretextmap/tests/main.nf.test +++ b/modules/nf-core/pretextmap/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true) @@ -41,6 +42,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true) @@ -68,6 +70,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) @@ -95,6 +98,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file("https://raw.githubusercontent.com/4dn-dcic/pairix/master/samples/test_4dn.pairs.gz", checkIfExists: true) @@ -122,6 +126,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end: false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true) diff --git a/modules/nf-core/prinseqplusplus/tests/main.nf.test b/modules/nf-core/prinseqplusplus/tests/main.nf.test index a6708ce96a4..1ed35cdfe6f 100644 --- a/modules/nf-core/prinseqplusplus/tests/main.nf.test +++ b/modules/nf-core/prinseqplusplus/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ] @@ -44,6 +45,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ diff --git a/modules/nf-core/prodigal/tests/main.nf.test b/modules/nf-core/prodigal/tests/main.nf.test index 446bd0d1968..8927e2033b9 100644 --- a/modules/nf-core/prodigal/tests/main.nf.test +++ b/modules/nf-core/prodigal/tests/main.nf.test @@ -12,6 +12,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) @@ -33,6 +34,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) @@ -57,6 +59,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) @@ -81,6 +84,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) diff --git a/modules/nf-core/prokka/tests/main.nf.test b/modules/nf-core/prokka/tests/main.nf.test index dca19bba717..c1e6e0c63b6 100644 --- a/modules/nf-core/prokka/tests/main.nf.test +++ b/modules/nf-core/prokka/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.fromList([ tuple([ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)) diff --git a/modules/nf-core/propr/grea/tests/main.nf.test b/modules/nf-core/propr/grea/tests/main.nf.test index dd442b43459..819b2491427 100644 --- a/modules/nf-core/propr/grea/tests/main.nf.test +++ b/modules/nf-core/propr/grea/tests/main.nf.test @@ -44,6 +44,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = PROPR_PROPR.out.adj.collect{ meta, adj -> adj }.map{ adj -> [[ id: 'test_adj'], adj]} input[1] = MYGENE.out.gmt.collect{ meta, gmt -> gmt }.map{ gmt -> [[ id: 'test_gmt'], gmt]} """ diff --git a/modules/nf-core/propr/propd/tests/main.nf.test b/modules/nf-core/propr/propd/tests/main.nf.test index 9fcaf93af1b..4a8e3e5cb03 100755 --- a/modules/nf-core/propr/propd/tests/main.nf.test +++ b/modules/nf-core/propr/propd/tests/main.nf.test @@ -17,6 +17,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/mus_musculus/rnaseq_expression/SRP254919.salmon.merged.gene_counts.top1000cov.tsv") @@ -46,6 +47,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/mus_musculus/rnaseq_expression/SRP254919.salmon.merged.gene_counts.top1000cov.tsv") @@ -75,6 +77,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/mus_musculus/rnaseq_expression/SRP254919.salmon.merged.gene_counts.top1000cov.tsv") @@ -103,6 +106,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/mus_musculus/rnaseq_expression/SRP254919.salmon.merged.gene_counts.top1000cov.tsv") @@ -131,6 +135,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/mus_musculus/rnaseq_expression/SRP254919.salmon.merged.gene_counts.top1000cov.tsv") diff --git a/modules/nf-core/propr/propr/tests/main.nf.test b/modules/nf-core/propr/propr/tests/main.nf.test index 1f2e67fe5ef..b79966ab325 100644 --- a/modules/nf-core/propr/propr/tests/main.nf.test +++ b/modules/nf-core/propr/propr/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], //file(params.modules_testdata_base_path + 'genomics/mus_musculus/rnaseq_expression/SRP254919.salmon.merged.gene_counts.top1000cov.tsv', checkIfExists: true) @@ -42,6 +43,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/mus_musculus/rnaseq_expression/SRP254919.salmon.merged.gene_counts.top1000cov.tsv', checkIfExists: true) @@ -67,6 +69,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/mus_musculus/rnaseq_expression/SRP254919.salmon.merged.gene_counts.top1000cov.tsv', checkIfExists: true) @@ -93,6 +96,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/mus_musculus/rnaseq_expression/SRP254919.salmon.merged.gene_counts.top1000cov.tsv', checkIfExists: true) @@ -118,6 +122,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/mus_musculus/rnaseq_expression/SRP254919.salmon.merged.gene_counts.top1000cov.tsv', checkIfExists: true) @@ -143,6 +148,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/mus_musculus/rnaseq_expression/SRP254919.salmon.merged.gene_counts.top1000cov.tsv', checkIfExists: true) @@ -168,6 +174,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/mus_musculus/rnaseq_expression/SRP254919.salmon.merged.gene_counts.top1000cov.tsv") @@ -194,6 +201,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/mus_musculus/rnaseq_expression/SRP254919.salmon.merged.gene_counts.top1000cov.tsv") @@ -220,6 +228,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/mus_musculus/rnaseq_expression/SRP254919.salmon.merged.gene_counts.top1000cov.tsv") diff --git a/modules/nf-core/pureclip/tests/main.nf.test b/modules/nf-core/pureclip/tests/main.nf.test index d21248425e8..d7f55f60f50 100644 --- a/modules/nf-core/pureclip/tests/main.nf.test +++ b/modules/nf-core/pureclip/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) ], @@ -52,6 +53,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) ], @@ -90,6 +92,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) ], diff --git a/modules/nf-core/purecn/intervalfile/tests/main.nf.test b/modules/nf-core/purecn/intervalfile/tests/main.nf.test index a14a0cbb450..afe82194cb6 100644 --- a/modules/nf-core/purecn/intervalfile/tests/main.nf.test +++ b/modules/nf-core/purecn/intervalfile/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [[id: "test"], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed', checkIfExists: true)] input[1] = [[id: "fasta"], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true)] input[2] = "hg38" @@ -41,6 +42,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [[id: "test"], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed', checkIfExists: true)] input[1] = [[id: "fasta"], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true)] input[2] = "hg38" diff --git a/modules/nf-core/purecn/normaldb/tests/main.nf.test b/modules/nf-core/purecn/normaldb/tests/main.nf.test index c7cd65bb55a..a058490dfc8 100644 --- a/modules/nf-core/purecn/normaldb/tests/main.nf.test +++ b/modules/nf-core/purecn/normaldb/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], [ @@ -50,6 +51,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], [ diff --git a/modules/nf-core/purgedups/pbcstat/tests/main.nf.test b/modules/nf-core/purgedups/pbcstat/tests/main.nf.test index 29598cd9b0d..fd3331201a9 100644 --- a/modules/nf-core/purgedups/pbcstat/tests/main.nf.test +++ b/modules/nf-core/purgedups/pbcstat/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.paf', checkIfExists: true) diff --git a/modules/nf-core/purgedups/splitfa/tests/main.nf.test b/modules/nf-core/purgedups/splitfa/tests/main.nf.test index 33b43c0d003..af25ff440cf 100644 --- a/modules/nf-core/purgedups/splitfa/tests/main.nf.test +++ b/modules/nf-core/purgedups/splitfa/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) diff --git a/modules/nf-core/pydamage/analyze/tests/main.nf.test b/modules/nf-core/pydamage/analyze/tests/main.nf.test index 5cca7cf2e66..810f7b656a3 100644 --- a/modules/nf-core/pydamage/analyze/tests/main.nf.test +++ b/modules/nf-core/pydamage/analyze/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), diff --git a/modules/nf-core/pyrodigal/tests/main.nf.test b/modules/nf-core/pyrodigal/tests/main.nf.test index faa7c8ece69..d4abcdd85ed 100644 --- a/modules/nf-core/pyrodigal/tests/main.nf.test +++ b/modules/nf-core/pyrodigal/tests/main.nf.test @@ -12,6 +12,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) @@ -33,6 +34,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) @@ -61,6 +63,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) @@ -87,6 +90,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) diff --git a/modules/nf-core/qcat/tests/main.nf.test b/modules/nf-core/qcat/tests/main.nf.test index 840fe2001ed..5d5161ca539 100644 --- a/modules/nf-core/qcat/tests/main.nf.test +++ b/modules/nf-core/qcat/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ file("https://github.com/nf-core/test-datasets/raw/nanoseq/fastq/nondemultiplexed/sample_nobc_dx.fastq.gz", checkIfExists: true) ] @@ -43,6 +44,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ file("https://github.com/nf-core/test-datasets/raw/nanoseq/fastq/nondemultiplexed/sample_nobc_dx.fastq.gz", checkIfExists: true) ] diff --git a/modules/nf-core/qualimap/bamqc/tests/main.nf.test b/modules/nf-core/qualimap/bamqc/tests/main.nf.test index eec1a41a164..eec5526eea7 100644 --- a/modules/nf-core/qualimap/bamqc/tests/main.nf.test +++ b/modules/nf-core/qualimap/bamqc/tests/main.nf.test @@ -12,6 +12,7 @@ nextflow_process { when { process { """ + // testy mctestface gff = [] input[0] = Channel.of([ @@ -40,6 +41,7 @@ nextflow_process { when { process { """ + // testy mctestface gff = [] input[0] = Channel.of([ diff --git a/modules/nf-core/qualimap/bamqccram/tests/main.nf.test b/modules/nf-core/qualimap/bamqccram/tests/main.nf.test index da2f300d671..ec15955e4e9 100644 --- a/modules/nf-core/qualimap/bamqccram/tests/main.nf.test +++ b/modules/nf-core/qualimap/bamqccram/tests/main.nf.test @@ -12,6 +12,7 @@ nextflow_process { when { process { """ + // testy mctestface gff = [] input[0] = Channel.of([ @@ -45,6 +46,7 @@ nextflow_process { when { process { """ + // testy mctestface gff = [] input[0] = Channel.of([ diff --git a/modules/nf-core/qualimap/rnaseq/tests/main.nf.test b/modules/nf-core/qualimap/rnaseq/tests/main.nf.test index bfc4a330e1b..a2618961928 100644 --- a/modules/nf-core/qualimap/rnaseq/tests/main.nf.test +++ b/modules/nf-core/qualimap/rnaseq/tests/main.nf.test @@ -12,6 +12,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) @@ -43,6 +44,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) diff --git a/modules/nf-core/quartonotebook/tests/main.nf.test b/modules/nf-core/quartonotebook/tests/main.nf.test index 4fa0ac22001..cc92c050541 100644 --- a/modules/nf-core/quartonotebook/tests/main.nf.test +++ b/modules/nf-core/quartonotebook/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'generic/notebooks/quarto/quarto_r.qmd', checkIfExists: true) // Notebook @@ -42,6 +43,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'generic/notebooks/quarto/quarto_python.qmd', checkIfExists: true) // Notebook @@ -74,6 +76,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'generic/notebooks/quarto/quarto_r.qmd', checkIfExists: true) // Notebook @@ -101,6 +104,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'generic/notebooks/quarto/quarto_python.qmd', checkIfExists: true) // Notebook @@ -133,6 +137,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'generic/notebooks/rmarkdown/rmarkdown_notebook.Rmd', checkIfExists: true) // notebook @@ -160,6 +165,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'generic/notebooks/jupyter/ipython_notebook.ipynb', checkIfExists: true) // notebook @@ -189,6 +195,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'generic/notebooks/quarto/quarto_r.qmd', checkIfExists: true) // Notebook diff --git a/modules/nf-core/quast/tests/main.nf.test b/modules/nf-core/quast/tests/main.nf.test index 44655a526ac..a443ce6a730 100644 --- a/modules/nf-core/quast/tests/main.nf.test +++ b/modules/nf-core/quast/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id: 'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/contigs.fasta', checkIfExists: true) @@ -48,6 +49,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id: 'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/contigs.fasta', checkIfExists: true) @@ -78,6 +80,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id: 'test1' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/contigs.fasta', checkIfExists: true) diff --git a/modules/nf-core/quilt/quilt/tests/main.nf.test b/modules/nf-core/quilt/quilt/tests/main.nf.test index 2d80516df52..3386f10e4f6 100644 --- a/modules/nf-core/quilt/quilt/tests/main.nf.test +++ b/modules/nf-core/quilt/quilt/tests/main.nf.test @@ -43,6 +43,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = $ch_input_gmap input[1] = $posfile_phasefile input[2] = $fasta @@ -64,6 +65,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = $ch_input_nogmap input[1] = [[id: null], [], []] input[2] = $fasta @@ -85,6 +87,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = $ch_input_gmap input[1] = $posfile_phasefile input[2] = $fasta @@ -113,6 +116,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = $ch_input_gmap input[1] = $posfile_phasefile input[2] = $fasta diff --git a/modules/nf-core/racon/tests/main.nf.test b/modules/nf-core/racon/tests/main.nf.test index 85e0469c2f5..2a4bb2cfb1c 100644 --- a/modules/nf-core/racon/tests/main.nf.test +++ b/modules/nf-core/racon/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/nanopore/fastq/test.fastq.gz', checkIfExists: true), diff --git a/modules/nf-core/rapidnj/tests/main.nf.test b/modules/nf-core/rapidnj/tests/main.nf.test index 8bd5bd7d0da..88e0ded84b4 100644 --- a/modules/nf-core/rapidnj/tests/main.nf.test +++ b/modules/nf-core/rapidnj/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/informative_sites.fas', checkIfExists: true) ] """ diff --git a/modules/nf-core/raven/tests/main.nf.test b/modules/nf-core/raven/tests/main.nf.test index cddfa418308..9948dc88900 100644 --- a/modules/nf-core/raven/tests/main.nf.test +++ b/modules/nf-core/raven/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/nanopore/fastq/test.fastq.gz', checkIfExists: true) ] diff --git a/modules/nf-core/repeatmodeler/builddatabase/tests/main.nf.test b/modules/nf-core/repeatmodeler/builddatabase/tests/main.nf.test index 78b78a68414..5bcd4c3fc3a 100644 --- a/modules/nf-core/repeatmodeler/builddatabase/tests/main.nf.test +++ b/modules/nf-core/repeatmodeler/builddatabase/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) @@ -40,6 +41,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) diff --git a/modules/nf-core/repeatmodeler/repeatmodeler/tests/main.nf.test b/modules/nf-core/repeatmodeler/repeatmodeler/tests/main.nf.test index 829e2221836..ec951ec92f4 100644 --- a/modules/nf-core/repeatmodeler/repeatmodeler/tests/main.nf.test +++ b/modules/nf-core/repeatmodeler/repeatmodeler/tests/main.nf.test @@ -30,6 +30,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = REPEATMODELER_BUILDDATABASE.out.db """ } @@ -54,6 +55,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) diff --git a/modules/nf-core/resfinder/run/tests/main.nf.test b/modules/nf-core/resfinder/run/tests/main.nf.test index 28f8688594c..4f7744e708a 100644 --- a/modules/nf-core/resfinder/run/tests/main.nf.test +++ b/modules/nf-core/resfinder/run/tests/main.nf.test @@ -30,6 +30,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map @@ -70,6 +71,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map @@ -111,6 +113,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map @@ -153,6 +156,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map diff --git a/modules/nf-core/rgi/cardannotation/tests/main.nf.test b/modules/nf-core/rgi/cardannotation/tests/main.nf.test index fa51142aa75..f42e15da143 100644 --- a/modules/nf-core/rgi/cardannotation/tests/main.nf.test +++ b/modules/nf-core/rgi/cardannotation/tests/main.nf.test @@ -31,6 +31,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = UNTAR.out.untar.map{ it[1] } """ } @@ -51,6 +52,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = UNTAR.out.untar.map{ it[1] } """ } diff --git a/modules/nf-core/rgi/main/tests/main.nf.test b/modules/nf-core/rgi/main/tests/main.nf.test index 1fca563a969..321a5c16245 100644 --- a/modules/nf-core/rgi/main/tests/main.nf.test +++ b/modules/nf-core/rgi/main/tests/main.nf.test @@ -42,6 +42,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.test_data['haemophilus_influenzae']['genome']['genome_fna_gz'], checkIfExists: true) @@ -74,6 +75,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.test_data['haemophilus_influenzae']['genome']['genome_fna_gz'], checkIfExists: true) diff --git a/modules/nf-core/rhocall/viz/tests/main.nf.test b/modules/nf-core/rhocall/viz/tests/main.nf.test index d2661e01b60..42ce51b7478 100644 --- a/modules/nf-core/rhocall/viz/tests/main.nf.test +++ b/modules/nf-core/rhocall/viz/tests/main.nf.test @@ -36,6 +36,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true)] input[1] = BCFTOOLS_ROH.out.roh diff --git a/modules/nf-core/ribotish/predict/tests/main.nf.test b/modules/nf-core/ribotish/predict/tests/main.nf.test index 41166616132..e9fc7381095 100644 --- a/modules/nf-core/ribotish/predict/tests/main.nf.test +++ b/modules/nf-core/ribotish/predict/tests/main.nf.test @@ -29,6 +29,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true, strandedness:'forward' ], // meta map file(params.modules_testdata_base_path + "genomics/homo_sapiens/riboseq_expression/aligned_reads/SRX11780888_chr20.bam", checkIfExists: true), @@ -65,6 +66,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true, strandedness:'forward' ], // meta map file(params.modules_testdata_base_path + "genomics/homo_sapiens/riboseq_expression/aligned_reads/SRX11780888_chr20.bam", checkIfExists: true), @@ -99,6 +101,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true, strandedness:'forward' ], // meta map [ @@ -141,6 +144,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true, strandedness:'forward' ], // meta map [ diff --git a/modules/nf-core/ribotish/quality/tests/main.nf.test b/modules/nf-core/ribotish/quality/tests/main.nf.test index 577c1bb31bf..1b51a6c17f1 100644 --- a/modules/nf-core/ribotish/quality/tests/main.nf.test +++ b/modules/nf-core/ribotish/quality/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true, strandedness:'forward' ], // meta map file(params.modules_testdata_base_path + "genomics/homo_sapiens/riboseq_expression/aligned_reads/SRX11780888_chr20.bam", checkIfExists: true), @@ -42,6 +43,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true, strandedness:'forward' ], // meta map file(params.modules_testdata_base_path + "genomics/homo_sapiens/riboseq_expression/aligned_reads/SRX11780888_chr20.bam", checkIfExists: true), diff --git a/modules/nf-core/ribotricer/detectorfs/tests/main.nf.test b/modules/nf-core/ribotricer/detectorfs/tests/main.nf.test index 540a32e412a..da8d6878151 100644 --- a/modules/nf-core/ribotricer/detectorfs/tests/main.nf.test +++ b/modules/nf-core/ribotricer/detectorfs/tests/main.nf.test @@ -45,6 +45,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true, strandedness:'forward' ], // meta map file(params.modules_testdata_base_path + "genomics/homo_sapiens/riboseq_expression/aligned_reads/SRX11780888_chr20.bam", checkIfExists: true), @@ -80,6 +81,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true, strandedness:'reverse' ], // meta map file(params.modules_testdata_base_path + "genomics/homo_sapiens/riboseq_expression/aligned_reads/SRX11780888_chr20.bam", checkIfExists: true), @@ -115,6 +117,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map file(params.modules_testdata_base_path + "genomics/homo_sapiens/riboseq_expression/aligned_reads/SRX11780888_chr20.bam", checkIfExists: true), @@ -150,6 +153,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true, strandedness:'forward' ], // meta map file(params.modules_testdata_base_path + "genomics/homo_sapiens/riboseq_expression/aligned_reads/SRX11780888_chr20.bam", checkIfExists: true), @@ -188,6 +192,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true, strandedness:'forward' ], // meta map file(params.modules_testdata_base_path + "genomics/homo_sapiens/riboseq_expression/aligned_reads/SRX11780888_chr20.bam", checkIfExists: true), @@ -225,6 +230,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true, strandedness:'reverse' ], // meta map file(params.modules_testdata_base_path + "genomics/homo_sapiens/riboseq_expression/aligned_reads/SRX11780888_chr20.bam", checkIfExists: true), @@ -262,6 +268,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map file(params.modules_testdata_base_path + "genomics/homo_sapiens/riboseq_expression/aligned_reads/SRX11780888_chr20.bam", checkIfExists: true), @@ -299,6 +306,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true, strandedness:'forward' ], // meta map file(params.modules_testdata_base_path + "genomics/homo_sapiens/riboseq_expression/aligned_reads/SRX11780888_chr20.bam", checkIfExists: true), diff --git a/modules/nf-core/ribotricer/prepareorfs/tests/main.nf.test b/modules/nf-core/ribotricer/prepareorfs/tests/main.nf.test index 752fc6e8bae..afef654ec72 100644 --- a/modules/nf-core/ribotricer/prepareorfs/tests/main.nf.test +++ b/modules/nf-core/ribotricer/prepareorfs/tests/main.nf.test @@ -29,6 +29,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = GUNZIP.out.gunzip.map{[ [id:'homo_sapiens_chr20'], it[1], @@ -53,6 +54,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = GUNZIP.out.gunzip.map{[ [id:'homo_sapiens_chr20'], it[1], diff --git a/modules/nf-core/ribowaltz/tests/main.nf.test b/modules/nf-core/ribowaltz/tests/main.nf.test index ace571ca6e6..6e70440c4aa 100644 --- a/modules/nf-core/ribowaltz/tests/main.nf.test +++ b/modules/nf-core/ribowaltz/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true, strandedness:'forward' ], // meta map file(params.modules_testdata_base_path + "genomics/homo_sapiens/riboseq_expression/aligned_reads/SRX11780888.Aligned.toTranscriptome.out.bam", checkIfExists: true) @@ -48,6 +49,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true, strandedness:'forward' ], // meta map file(params.modules_testdata_base_path + "genomics/homo_sapiens/riboseq_expression/aligned_reads/SRX11780888.Aligned.toTranscriptome.out.bam", checkIfExists: true) diff --git a/modules/nf-core/rrnatranscripts/tests/main.nf.test b/modules/nf-core/rrnatranscripts/tests/main.nf.test index db0d5565224..9dc9e27234c 100644 --- a/modules/nf-core/rrnatranscripts/tests/main.nf.test +++ b/modules/nf-core/rrnatranscripts/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] """ @@ -35,6 +36,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] """ diff --git a/modules/nf-core/rsem/calculateexpression/tests/main.nf.test b/modules/nf-core/rsem/calculateexpression/tests/main.nf.test index 5df41c0b8b6..ac6b28ffe7a 100644 --- a/modules/nf-core/rsem/calculateexpression/tests/main.nf.test +++ b/modules/nf-core/rsem/calculateexpression/tests/main.nf.test @@ -72,6 +72,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', strandedness: 'forward' ], // meta map [ diff --git a/modules/nf-core/rsem/preparereference/tests/main.nf.test b/modules/nf-core/rsem/preparereference/tests/main.nf.test index 9f618ad4cee..dce4fd156d5 100644 --- a/modules/nf-core/rsem/preparereference/tests/main.nf.test +++ b/modules/nf-core/rsem/preparereference/tests/main.nf.test @@ -39,6 +39,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)) input[1] = Channel.of(file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true)) """ diff --git a/modules/nf-core/rseqc/bamstat/tests/main.nf.test b/modules/nf-core/rseqc/bamstat/tests/main.nf.test index 86f4301e983..1470adf2c56 100644 --- a/modules/nf-core/rseqc/bamstat/tests/main.nf.test +++ b/modules/nf-core/rseqc/bamstat/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam') @@ -37,6 +38,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam') diff --git a/modules/nf-core/rseqc/inferexperiment/tests/main.nf.test b/modules/nf-core/rseqc/inferexperiment/tests/main.nf.test index f07384442c4..19ec2cc239e 100644 --- a/modules/nf-core/rseqc/inferexperiment/tests/main.nf.test +++ b/modules/nf-core/rseqc/inferexperiment/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test' ], // meta map file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true) @@ -37,6 +38,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test' ], // meta map file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true) diff --git a/modules/nf-core/rseqc/innerdistance/tests/main.nf.test b/modules/nf-core/rseqc/innerdistance/tests/main.nf.test index cb19fe14499..ccaf3c4e7ef 100644 --- a/modules/nf-core/rseqc/innerdistance/tests/main.nf.test +++ b/modules/nf-core/rseqc/innerdistance/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test' ], // meta map file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true) @@ -44,6 +45,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test' ], // meta map file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true) diff --git a/modules/nf-core/rseqc/junctionannotation/tests/main.nf.test b/modules/nf-core/rseqc/junctionannotation/tests/main.nf.test index 36d5f6e237d..e707b0dfe75 100644 --- a/modules/nf-core/rseqc/junctionannotation/tests/main.nf.test +++ b/modules/nf-core/rseqc/junctionannotation/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end: false ], // meta map file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true) @@ -41,6 +42,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end: false ], // meta map file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true) diff --git a/modules/nf-core/rseqc/junctionsaturation/tests/main.nf.test b/modules/nf-core/rseqc/junctionsaturation/tests/main.nf.test index 7bd3cfc20a5..914cc852043 100644 --- a/modules/nf-core/rseqc/junctionsaturation/tests/main.nf.test +++ b/modules/nf-core/rseqc/junctionsaturation/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end: false ], // meta map file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true) @@ -40,6 +41,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end: false ], // meta map file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true) diff --git a/modules/nf-core/rseqc/readdistribution/tests/main.nf.test b/modules/nf-core/rseqc/readdistribution/tests/main.nf.test index 5fa76950cb1..96a75ed80d2 100644 --- a/modules/nf-core/rseqc/readdistribution/tests/main.nf.test +++ b/modules/nf-core/rseqc/readdistribution/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end: false ], // meta map file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true) @@ -37,6 +38,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end: false ], // meta map file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true) diff --git a/modules/nf-core/rseqc/readduplication/tests/main.nf.test b/modules/nf-core/rseqc/readduplication/tests/main.nf.test index 334a4e670f2..5786be5a5de 100644 --- a/modules/nf-core/rseqc/readduplication/tests/main.nf.test +++ b/modules/nf-core/rseqc/readduplication/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end: false ], // meta map file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true) @@ -40,6 +41,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end: false ], // meta map file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true) diff --git a/modules/nf-core/rseqc/tin/tests/main.nf.test b/modules/nf-core/rseqc/tin/tests/main.nf.test index b11eba80bd5..579e3f32d5f 100644 --- a/modules/nf-core/rseqc/tin/tests/main.nf.test +++ b/modules/nf-core/rseqc/tin/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true), @@ -38,6 +39,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true), diff --git a/modules/nf-core/rtgtools/pedfilter/tests/main.nf.test b/modules/nf-core/rtgtools/pedfilter/tests/main.nf.test index 0ddcebdbaf7..5cf52e62fdc 100644 --- a/modules/nf-core/rtgtools/pedfilter/tests/main.nf.test +++ b/modules/nf-core/rtgtools/pedfilter/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/ped/justhusky.ped', checkIfExists: true) @@ -37,6 +38,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz', checkIfExists: true) @@ -61,6 +63,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/ped/justhusky.ped', checkIfExists: true) diff --git a/modules/nf-core/rtgtools/vcfeval/tests/main.nf.test b/modules/nf-core/rtgtools/vcfeval/tests/main.nf.test index 55abc842759..03cf0e0cdbf 100644 --- a/modules/nf-core/rtgtools/vcfeval/tests/main.nf.test +++ b/modules/nf-core/rtgtools/vcfeval/tests/main.nf.test @@ -29,6 +29,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [id:'test'], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.vcf.gz', checkIfExists:true), @@ -57,6 +58,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [id:'test'], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.vcf.gz', checkIfExists:true), @@ -87,6 +89,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [id:'test'], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.vcf.gz', checkIfExists:true), diff --git a/modules/nf-core/rtn/tni/tests/main.nf.test b/modules/nf-core/rtn/tni/tests/main.nf.test index d695981acc3..334ff66167c 100644 --- a/modules/nf-core/rtn/tni/tests/main.nf.test +++ b/modules/nf-core/rtn/tni/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id:'test'], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/riboseq_expression/salmon.merged.gene_counts_length_scaled.tsv', checkIfExists: true) @@ -124,6 +125,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id:'test'], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/riboseq_expression/salmon.merged.gene_counts_length_scaled.tsv', checkIfExists: true) diff --git a/modules/nf-core/sageproteomics/sage/tests/main.nf.test b/modules/nf-core/sageproteomics/sage/tests/main.nf.test index 4f48ee20d39..c302df89f99 100644 --- a/modules/nf-core/sageproteomics/sage/tests/main.nf.test +++ b/modules/nf-core/sageproteomics/sage/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test'], // meta map file(params.modules_testdata_base_path + 'proteomics/msspectra/peakpicker_tutorial_1.mzML', checkIfExists: true) @@ -42,6 +43,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test'], // meta map file(params.modules_testdata_base_path + 'proteomics/msspectra/peakpicker_tutorial_1.mzML', checkIfExists: true) diff --git a/modules/nf-core/salsa2/tests/main.nf.test b/modules/nf-core/salsa2/tests/main.nf.test index 6897f231430..758b2e2952c 100644 --- a/modules/nf-core/salsa2/tests/main.nf.test +++ b/modules/nf-core/salsa2/tests/main.nf.test @@ -12,6 +12,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end: false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true), diff --git a/modules/nf-core/sam2lca/analyze/tests/main.nf.test b/modules/nf-core/sam2lca/analyze/tests/main.nf.test index 25ff02a51fc..b28754847af 100644 --- a/modules/nf-core/sam2lca/analyze/tests/main.nf.test +++ b/modules/nf-core/sam2lca/analyze/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file("https://raw.githubusercontent.com/maxibor/sam2lca/1.1.2/tests/data/microtest.sorted.bam", checkIfExists: true), @@ -47,6 +48,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file("https://raw.githubusercontent.com/maxibor/sam2lca/1.1.2/tests/data/microtest.sorted.bam", checkIfExists: true), diff --git a/modules/nf-core/sambamba/flagstat/tests/main.nf.test b/modules/nf-core/sambamba/flagstat/tests/main.nf.test index 95c57057aeb..65837ba2063 100644 --- a/modules/nf-core/sambamba/flagstat/tests/main.nf.test +++ b/modules/nf-core/sambamba/flagstat/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) diff --git a/modules/nf-core/sambamba/markdup/tests/main.nf.test b/modules/nf-core/sambamba/markdup/tests/main.nf.test index 9257fd21d40..c722fe8802d 100644 --- a/modules/nf-core/sambamba/markdup/tests/main.nf.test +++ b/modules/nf-core/sambamba/markdup/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) diff --git a/modules/nf-core/samblaster/tests/main.nf.test b/modules/nf-core/samblaster/tests/main.nf.test index 20d505bbef0..d21a08f1390 100644 --- a/modules/nf-core/samblaster/tests/main.nf.test +++ b/modules/nf-core/samblaster/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/umi/test.paired_end.umi_unsorted.bam', checkIfExists: true) @@ -42,6 +43,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/umi/test.paired_end.umi_unsorted.bam', checkIfExists: true) diff --git a/modules/nf-core/samtools/ampliconclip/tests/main.nf.test b/modules/nf-core/samtools/ampliconclip/tests/main.nf.test index abb0fd01fb8..3a82f6f80f4 100644 --- a/modules/nf-core/samtools/ampliconclip/tests/main.nf.test +++ b/modules/nf-core/samtools/ampliconclip/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface save_cliprejects = false save_clipstats = false @@ -45,6 +46,7 @@ nextflow_process { when { process { """ + // testy mctestface save_cliprejects = true save_clipstats = false @@ -75,6 +77,7 @@ nextflow_process { when { process { """ + // testy mctestface save_cliprejects = true save_clipstats = true diff --git a/modules/nf-core/samtools/bam2fq/tests/main.nf.test b/modules/nf-core/samtools/bam2fq/tests/main.nf.test index 0601af8bc7c..eee66fed8ba 100644 --- a/modules/nf-core/samtools/bam2fq/tests/main.nf.test +++ b/modules/nf-core/samtools/bam2fq/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface split = false input[0] = Channel.of([ @@ -42,6 +43,7 @@ nextflow_process { when { process { """ + // testy mctestface split = true input[0] = Channel.of([ diff --git a/modules/nf-core/samtools/calmd/tests/main.nf.test b/modules/nf-core/samtools/calmd/tests/main.nf.test index a2fa0cabb33..5c7958619fa 100644 --- a/modules/nf-core/samtools/calmd/tests/main.nf.test +++ b/modules/nf-core/samtools/calmd/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) @@ -43,6 +44,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) diff --git a/modules/nf-core/samtools/cat/tests/main.nf.test b/modules/nf-core/samtools/cat/tests/main.nf.test index dad80b83df3..f4edd0f2da0 100644 --- a/modules/nf-core/samtools/cat/tests/main.nf.test +++ b/modules/nf-core/samtools/cat/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [id: 'test', single_end: false], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true), @@ -40,6 +41,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [id: 'test', single_end: false], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true), diff --git a/modules/nf-core/samtools/collate/tests/main.nf.test b/modules/nf-core/samtools/collate/tests/main.nf.test index 875f0e9a3d6..bba96d2ce95 100644 --- a/modules/nf-core/samtools/collate/tests/main.nf.test +++ b/modules/nf-core/samtools/collate/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) @@ -40,6 +41,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true) diff --git a/modules/nf-core/samtools/collatefastq/tests/main.nf.test b/modules/nf-core/samtools/collatefastq/tests/main.nf.test index bc66ebf6e30..105017dccf9 100644 --- a/modules/nf-core/samtools/collatefastq/tests/main.nf.test +++ b/modules/nf-core/samtools/collatefastq/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) @@ -42,6 +43,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.bam', checkIfExists: true) @@ -70,6 +72,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true) @@ -98,6 +101,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) @@ -128,6 +132,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) @@ -156,6 +161,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.bam', checkIfExists: true) @@ -184,6 +190,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true) @@ -212,6 +219,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) diff --git a/modules/nf-core/samtools/consensus/tests/main.nf.test b/modules/nf-core/samtools/consensus/tests/main.nf.test index 85163731d56..c4a01b6a480 100644 --- a/modules/nf-core/samtools/consensus/tests/main.nf.test +++ b/modules/nf-core/samtools/consensus/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [id: 'test', single_end: false], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) @@ -36,6 +37,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [id: 'test', single_end: false], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), ]) @@ -57,6 +59,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [id: 'test', single_end: false], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) ]) @@ -80,6 +83,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [id: 'test', single_end: false], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), ]) diff --git a/modules/nf-core/samtools/convert/tests/main.nf.test b/modules/nf-core/samtools/convert/tests/main.nf.test index 91a0c69ea1d..d7e21c660d0 100644 --- a/modules/nf-core/samtools/convert/tests/main.nf.test +++ b/modules/nf-core/samtools/convert/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [id: 'test', single_end: false], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), @@ -46,6 +47,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [id: 'test', single_end: false], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), @@ -80,6 +82,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [id: 'test', single_end: false], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), diff --git a/modules/nf-core/samtools/coverage/tests/main.nf.test b/modules/nf-core/samtools/coverage/tests/main.nf.test index 1e3ad5a4791..9a2ba2610b2 100644 --- a/modules/nf-core/samtools/coverage/tests/main.nf.test +++ b/modules/nf-core/samtools/coverage/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [id: 'test', single_end: false], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), @@ -44,6 +45,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [id: 'test', single_end: false], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), @@ -76,6 +78,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [id: 'test', single_end: false], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), diff --git a/modules/nf-core/samtools/cramsize/tests/main.nf.test b/modules/nf-core/samtools/cramsize/tests/main.nf.test index c88ffd59c63..ee764f2dd03 100644 --- a/modules/nf-core/samtools/cramsize/tests/main.nf.test +++ b/modules/nf-core/samtools/cramsize/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [[ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true) ] @@ -37,6 +38,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [[ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true) ] diff --git a/modules/nf-core/samtools/depth/tests/main.nf.test b/modules/nf-core/samtools/depth/tests/main.nf.test index ddacb540748..43065871d67 100644 --- a/modules/nf-core/samtools/depth/tests/main.nf.test +++ b/modules/nf-core/samtools/depth/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam', checkIfExists: true) @@ -38,6 +39,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam', checkIfExists: true) diff --git a/modules/nf-core/samtools/dict/tests/main.nf.test b/modules/nf-core/samtools/dict/tests/main.nf.test index c467081f82f..1d5eccc852a 100644 --- a/modules/nf-core/samtools/dict/tests/main.nf.test +++ b/modules/nf-core/samtools/dict/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) @@ -42,6 +43,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) diff --git a/modules/nf-core/samtools/faidx/tests/main.nf.test b/modules/nf-core/samtools/faidx/tests/main.nf.test index 17244ef2ee3..f126cc87d9f 100644 --- a/modules/nf-core/samtools/faidx/tests/main.nf.test +++ b/modules/nf-core/samtools/faidx/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] @@ -35,6 +36,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true)] @@ -58,6 +60,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] @@ -82,6 +85,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] @@ -104,6 +108,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] diff --git a/modules/nf-core/samtools/fasta/tests/main.nf.test b/modules/nf-core/samtools/fasta/tests/main.nf.test index 30d0c25a052..5bbd2730758 100644 --- a/modules/nf-core/samtools/fasta/tests/main.nf.test +++ b/modules/nf-core/samtools/fasta/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) @@ -44,6 +45,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) diff --git a/modules/nf-core/samtools/fastq/tests/main.nf.test b/modules/nf-core/samtools/fastq/tests/main.nf.test index f6ac1123f2d..b938b25686a 100644 --- a/modules/nf-core/samtools/fastq/tests/main.nf.test +++ b/modules/nf-core/samtools/fastq/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface interleave = false input[0] = Channel.of([ @@ -42,6 +43,7 @@ nextflow_process { when { process { """ + // testy mctestface interleave = true input[0] = Channel.of([ diff --git a/modules/nf-core/samtools/fixmate/tests/main.nf.test b/modules/nf-core/samtools/fixmate/tests/main.nf.test index ee3bc55449f..a745b7aa0c2 100644 --- a/modules/nf-core/samtools/fixmate/tests/main.nf.test +++ b/modules/nf-core/samtools/fixmate/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) diff --git a/modules/nf-core/samtools/flagstat/tests/main.nf.test b/modules/nf-core/samtools/flagstat/tests/main.nf.test index 3b648a37d55..8f643718c05 100644 --- a/modules/nf-core/samtools/flagstat/tests/main.nf.test +++ b/modules/nf-core/samtools/flagstat/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), @@ -37,6 +38,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), diff --git a/modules/nf-core/samtools/getrg/tests/main.nf.test b/modules/nf-core/samtools/getrg/tests/main.nf.test index 03c25450020..cd678f815db 100644 --- a/modules/nf-core/samtools/getrg/tests/main.nf.test +++ b/modules/nf-core/samtools/getrg/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) diff --git a/modules/nf-core/samtools/idxstats/tests/main.nf.test b/modules/nf-core/samtools/idxstats/tests/main.nf.test index 5fd1fc78ef4..0305693e06c 100644 --- a/modules/nf-core/samtools/idxstats/tests/main.nf.test +++ b/modules/nf-core/samtools/idxstats/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), @@ -35,6 +36,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), diff --git a/modules/nf-core/samtools/index/tests/main.nf.test b/modules/nf-core/samtools/index/tests/main.nf.test index ca34fb5cd41..b8057bc9e81 100644 --- a/modules/nf-core/samtools/index/tests/main.nf.test +++ b/modules/nf-core/samtools/index/tests/main.nf.test @@ -12,6 +12,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) @@ -32,6 +33,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram', checkIfExists: true) @@ -54,6 +56,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) @@ -78,6 +81,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) @@ -99,6 +103,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram', checkIfExists: true) @@ -122,6 +127,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) diff --git a/modules/nf-core/samtools/markdup/tests/main.nf.test b/modules/nf-core/samtools/markdup/tests/main.nf.test index acfbd1c166e..d580b53a30c 100644 --- a/modules/nf-core/samtools/markdup/tests/main.nf.test +++ b/modules/nf-core/samtools/markdup/tests/main.nf.test @@ -41,6 +41,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = SAMTOOLS_SORT.out.bam input[1] = [ [ id:'fasta' ], @@ -66,6 +67,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), diff --git a/modules/nf-core/samtools/merge/tests/main.nf.test b/modules/nf-core/samtools/merge/tests/main.nf.test index 40b36e82b19..85cbfc71b4b 100644 --- a/modules/nf-core/samtools/merge/tests/main.nf.test +++ b/modules/nf-core/samtools/merge/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam', checkIfExists: true), @@ -47,6 +48,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram', checkIfExists: true), @@ -81,6 +83,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam', checkIfExists: true) ] @@ -111,6 +114,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam', checkIfExists: true), diff --git a/modules/nf-core/samtools/mpileup/tests/main.nf.test b/modules/nf-core/samtools/mpileup/tests/main.nf.test index d9cd6d804d5..2089a7a73a0 100644 --- a/modules/nf-core/samtools/mpileup/tests/main.nf.test +++ b/modules/nf-core/samtools/mpileup/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), @@ -38,6 +39,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), diff --git a/modules/nf-core/samtools/reheader/tests/main.nf.test b/modules/nf-core/samtools/reheader/tests/main.nf.test index 53142525d15..9b02762b610 100644 --- a/modules/nf-core/samtools/reheader/tests/main.nf.test +++ b/modules/nf-core/samtools/reheader/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), @@ -36,6 +37,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), @@ -60,6 +62,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), diff --git a/modules/nf-core/samtools/sormadup/tests/main.nf.test b/modules/nf-core/samtools/sormadup/tests/main.nf.test index 031b022f88f..48594edad36 100644 --- a/modules/nf-core/samtools/sormadup/tests/main.nf.test +++ b/modules/nf-core/samtools/sormadup/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [id: 'test', single_end: false], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), @@ -41,6 +42,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [id: 'test', single_end: false], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), diff --git a/modules/nf-core/samtools/sort/tests/main.nf.test b/modules/nf-core/samtools/sort/tests/main.nf.test index 0bc6c835842..cad5041f931 100644 --- a/modules/nf-core/samtools/sort/tests/main.nf.test +++ b/modules/nf-core/samtools/sort/tests/main.nf.test @@ -47,6 +47,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true) @@ -79,6 +80,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) @@ -107,6 +109,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true) diff --git a/modules/nf-core/samtools/stats/tests/main.nf.test b/modules/nf-core/samtools/stats/tests/main.nf.test index 5bc89309592..03b1c136b8c 100644 --- a/modules/nf-core/samtools/stats/tests/main.nf.test +++ b/modules/nf-core/samtools/stats/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), @@ -37,6 +38,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram', checkIfExists: true), @@ -65,6 +67,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), @@ -90,6 +93,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram', checkIfExists: true), diff --git a/modules/nf-core/samtools/view/tests/main.nf.test b/modules/nf-core/samtools/view/tests/main.nf.test index 37b81a91630..910be6c1973 100644 --- a/modules/nf-core/samtools/view/tests/main.nf.test +++ b/modules/nf-core/samtools/view/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true), @@ -44,6 +45,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), @@ -79,6 +81,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), @@ -114,6 +117,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), @@ -149,6 +153,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), @@ -187,6 +192,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true), diff --git a/modules/nf-core/scimap/mcmicro/tests/main.nf.test b/modules/nf-core/scimap/mcmicro/tests/main.nf.test index 79728d53ff4..060905d297f 100644 --- a/modules/nf-core/scimap/mcmicro/tests/main.nf.test +++ b/modules/nf-core/scimap/mcmicro/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'imaging/downstream/cycif_tonsil_cell.csv', checkIfExists: true) @@ -43,6 +44,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'imaging/downstream/cycif_tonsil_cell.csv', checkIfExists: true) diff --git a/modules/nf-core/scimap/spatiallda/tests/main.nf.test b/modules/nf-core/scimap/spatiallda/tests/main.nf.test index 688977ab305..5a2289bb8cf 100644 --- a/modules/nf-core/scimap/spatiallda/tests/main.nf.test +++ b/modules/nf-core/scimap/spatiallda/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'imaging/downstream/phenotyped.csv', checkIfExists: true) @@ -37,6 +38,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'imaging/downstream/phenotyped.csv', checkIfExists: true) diff --git a/modules/nf-core/scoary/tests/main.nf.test b/modules/nf-core/scoary/tests/main.nf.test index a3023dd68bb..ea6c5381e4a 100644 --- a/modules/nf-core/scoary/tests/main.nf.test +++ b/modules/nf-core/scoary/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file("https://github.com/AdmiralenOla/Scoary/raw/master/scoary/exampledata/Gene_presence_absence.csv", checkIfExists: true), file("https://github.com/AdmiralenOla/Scoary/raw/master/scoary/exampledata/Tetracycline_resistance.csv", checkIfExists: true) diff --git a/modules/nf-core/scramble/clusteridentifier/tests/main.nf.test b/modules/nf-core/scramble/clusteridentifier/tests/main.nf.test index fd273e68eee..8616e6d29ec 100644 --- a/modules/nf-core/scramble/clusteridentifier/tests/main.nf.test +++ b/modules/nf-core/scramble/clusteridentifier/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/scramble/test.bam', checkIfExists: true), @@ -39,6 +40,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/scramble/test.cram', checkIfExists: true), diff --git a/modules/nf-core/seacr/callpeak/tests/main.nf.test b/modules/nf-core/seacr/callpeak/tests/main.nf.test index 8db00114648..3b8305fb15c 100644 --- a/modules/nf-core/seacr/callpeak/tests/main.nf.test +++ b/modules/nf-core/seacr/callpeak/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test_1'], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bedgraph/cutandtag_h3k27me3_test_1.bedGraph', checkIfExists: true), @@ -40,6 +41,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test_1'], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bedgraph/cutandtag_h3k27me3_test_1.bedGraph', checkIfExists: true), diff --git a/modules/nf-core/segemehl/align/tests/main.nf.test b/modules/nf-core/segemehl/align/tests/main.nf.test index c1b4921e773..d22da3b95db 100644 --- a/modules/nf-core/segemehl/align/tests/main.nf.test +++ b/modules/nf-core/segemehl/align/tests/main.nf.test @@ -26,6 +26,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:true ], // meta map [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true) ] @@ -51,6 +52,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map [ @@ -81,6 +83,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:true ], // meta map [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true) ] @@ -111,6 +114,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map [ diff --git a/modules/nf-core/segemehl/index/tests/main.nf.test b/modules/nf-core/segemehl/index/tests/main.nf.test index fd6e8f29fe8..ee13bd2a36b 100644 --- a/modules/nf-core/segemehl/index/tests/main.nf.test +++ b/modules/nf-core/segemehl/index/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) """ @@ -34,6 +35,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) """ diff --git a/modules/nf-core/sentieon/bwamem/tests/main.nf.test b/modules/nf-core/sentieon/bwamem/tests/main.nf.test index 074722882c4..d705ee89923 100644 --- a/modules/nf-core/sentieon/bwamem/tests/main.nf.test +++ b/modules/nf-core/sentieon/bwamem/tests/main.nf.test @@ -32,6 +32,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map [ @@ -74,6 +75,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map [ @@ -116,6 +118,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ @@ -133,6 +136,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ @@ -176,6 +180,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map [ @@ -219,6 +224,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ @@ -236,6 +242,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ diff --git a/modules/nf-core/sentieon/collectvcmetrics/tests/main.nf.test b/modules/nf-core/sentieon/collectvcmetrics/tests/main.nf.test index 2b1ada4cebf..fdd7ae881c9 100644 --- a/modules/nf-core/sentieon/collectvcmetrics/tests/main.nf.test +++ b/modules/nf-core/sentieon/collectvcmetrics/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true) ], @@ -53,6 +54,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true) ], @@ -91,6 +93,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], [], [] ] diff --git a/modules/nf-core/sentieon/coveragemetrics/tests/main.nf.test b/modules/nf-core/sentieon/coveragemetrics/tests/main.nf.test index 8b9b86a7284..f218c994ec0 100644 --- a/modules/nf-core/sentieon/coveragemetrics/tests/main.nf.test +++ b/modules/nf-core/sentieon/coveragemetrics/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) ], @@ -43,6 +44,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) ], @@ -70,6 +72,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) ], @@ -97,6 +100,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) ], @@ -124,6 +128,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ @@ -158,6 +163,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [], diff --git a/modules/nf-core/sentieon/datametrics/tests/main.nf.test b/modules/nf-core/sentieon/datametrics/tests/main.nf.test index a13d68e6ef3..d542da9e652 100644 --- a/modules/nf-core/sentieon/datametrics/tests/main.nf.test +++ b/modules/nf-core/sentieon/datametrics/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), @@ -45,6 +46,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), @@ -79,6 +81,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), diff --git a/modules/nf-core/sentieon/dedup/tests/main.nf.test b/modules/nf-core/sentieon/dedup/tests/main.nf.test index c842a4a00cd..f1587422785 100644 --- a/modules/nf-core/sentieon/dedup/tests/main.nf.test +++ b/modules/nf-core/sentieon/dedup/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) ], @@ -42,6 +43,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) ], @@ -68,6 +70,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.sorted.bam', checkIfExists: true) ], diff --git a/modules/nf-core/sentieon/gvcftyper/tests/main.nf.test b/modules/nf-core/sentieon/gvcftyper/tests/main.nf.test index 0f66feb6810..3fb6fc22304 100644 --- a/modules/nf-core/sentieon/gvcftyper/tests/main.nf.test +++ b/modules/nf-core/sentieon/gvcftyper/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics//homo_sapiens/illumina/gvcf/test.genome.vcf.idx', checkIfExists: true), @@ -49,6 +50,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics//homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi', checkIfExists: true), @@ -83,6 +85,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics//homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi', checkIfExists: true), @@ -117,6 +120,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics//homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi', checkIfExists: true), @@ -151,6 +155,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics//homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi', checkIfExists: true), @@ -186,6 +191,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true), diff --git a/modules/nf-core/sentieon/haplotyper/tests/main.nf.test b/modules/nf-core/sentieon/haplotyper/tests/main.nf.test index c06ed175974..accceb1d55e 100644 --- a/modules/nf-core/sentieon/haplotyper/tests/main.nf.test +++ b/modules/nf-core/sentieon/haplotyper/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true), @@ -51,6 +52,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true), @@ -86,6 +88,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true), @@ -123,6 +126,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true), @@ -160,6 +164,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true), @@ -218,6 +223,7 @@ nextflow_process { when { process { """ + // testy mctestface recal_table = SENTIEON_QUALCAL.out.table bam = Channel.of([ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), @@ -255,6 +261,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ @@ -298,6 +305,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true), diff --git a/modules/nf-core/sentieon/qualcal/tests/main.nf.test b/modules/nf-core/sentieon/qualcal/tests/main.nf.test index 72c5564f4d4..b9d1cf533ea 100644 --- a/modules/nf-core/sentieon/qualcal/tests/main.nf.test +++ b/modules/nf-core/sentieon/qualcal/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam', checkIfExists: true), @@ -48,6 +49,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), @@ -99,6 +101,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), @@ -151,6 +154,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), @@ -181,6 +185,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), @@ -211,6 +216,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), diff --git a/modules/nf-core/sentieon/readwriter/tests/main.nf.test b/modules/nf-core/sentieon/readwriter/tests/main.nf.test index 9a787b44c25..14e259aad60 100644 --- a/modules/nf-core/sentieon/readwriter/tests/main.nf.test +++ b/modules/nf-core/sentieon/readwriter/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id: 'test' ], file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) @@ -44,6 +45,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id: 'test', fasta: params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta' ], file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true) @@ -73,6 +75,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id: 'test' ], [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), @@ -109,6 +112,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id: 'test', fasta: params.modules_testdata_base_path + '/genomics/sarscov2/genome/genome.fasta' ], [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), @@ -146,6 +150,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id: 'test' ], file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true) diff --git a/modules/nf-core/seqcluster/collapse/tests/main.nf.test b/modules/nf-core/seqcluster/collapse/tests/main.nf.test index ffca4e92579..02f96aa4cb9 100644 --- a/modules/nf-core/seqcluster/collapse/tests/main.nf.test +++ b/modules/nf-core/seqcluster/collapse/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test_1', single_end:false ], // meta map file("https://github.com/nf-core/test-datasets/raw/smrnaseq/testdata/trimmed/small_Clone1_N1.fastp.fastq.gz", checkIfExists: true), @@ -38,6 +39,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test_1', single_end:false ], // meta map file("https://github.com/nf-core/test-datasets/raw/smrnaseq/testdata/trimmed/small_Clone1_N1.fastp.fastq.gz", checkIfExists: true), diff --git a/modules/nf-core/seqfu/derep/tests/main.nf.test b/modules/nf-core/seqfu/derep/tests/main.nf.test index 60df330edea..c293e8bc17c 100644 --- a/modules/nf-core/seqfu/derep/tests/main.nf.test +++ b/modules/nf-core/seqfu/derep/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], [ @@ -40,6 +41,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of(">T1;size=300", "TTGATCACATA", ">T2;size=10", @@ -67,6 +69,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/proteome.fasta', checkIfExists: true) diff --git a/modules/nf-core/seqfu/stats/tests/main.nf.test b/modules/nf-core/seqfu/stats/tests/main.nf.test index b889b2bb9a8..dfc1bbec64d 100644 --- a/modules/nf-core/seqfu/stats/tests/main.nf.test +++ b/modules/nf-core/seqfu/stats/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/proteome.fasta', checkIfExists: true) @@ -42,6 +43,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], [ diff --git a/modules/nf-core/seqkit/concat/tests/main.nf.test b/modules/nf-core/seqkit/concat/tests/main.nf.test index 3ebae280cfb..8133ca89ee6 100644 --- a/modules/nf-core/seqkit/concat/tests/main.nf.test +++ b/modules/nf-core/seqkit/concat/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ @@ -45,6 +46,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ diff --git a/modules/nf-core/seqkit/fq2fa/tests/main.nf.test b/modules/nf-core/seqkit/fq2fa/tests/main.nf.test index 08f399e7a9c..e196ba12126 100644 --- a/modules/nf-core/seqkit/fq2fa/tests/main.nf.test +++ b/modules/nf-core/seqkit/fq2fa/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [[ id:'test', single_end:false ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ] ] @@ -37,6 +38,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [[ id:'test', single_end:false ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ] ] diff --git a/modules/nf-core/seqkit/fx2tab/tests/main.nf.test b/modules/nf-core/seqkit/fx2tab/tests/main.nf.test index 7e524e0833f..3b2fd737073 100644 --- a/modules/nf-core/seqkit/fx2tab/tests/main.nf.test +++ b/modules/nf-core/seqkit/fx2tab/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] ] @@ -35,6 +36,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ] ] @@ -58,6 +60,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ] ] diff --git a/modules/nf-core/seqkit/grep/tests/main.nf.test b/modules/nf-core/seqkit/grep/tests/main.nf.test index 93e4c07f389..79d7ccbfafa 100644 --- a/modules/nf-core/seqkit/grep/tests/main.nf.test +++ b/modules/nf-core/seqkit/grep/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [[ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true) ] @@ -36,6 +37,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [[ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true) ] @@ -60,6 +62,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [[ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true) ] diff --git a/modules/nf-core/seqkit/pair/tests/main.nf.test b/modules/nf-core/seqkit/pair/tests/main.nf.test index 4ced86ebf58..6ccd3be522e 100644 --- a/modules/nf-core/seqkit/pair/tests/main.nf.test +++ b/modules/nf-core/seqkit/pair/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ] @@ -38,6 +39,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ] diff --git a/modules/nf-core/seqkit/replace/tests/main.nf.test b/modules/nf-core/seqkit/replace/tests/main.nf.test index 759974c1bfc..aeaec9849ce 100644 --- a/modules/nf-core/seqkit/replace/tests/main.nf.test +++ b/modules/nf-core/seqkit/replace/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] ] @@ -39,6 +40,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] ] @@ -62,6 +64,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] ] diff --git a/modules/nf-core/seqkit/rmdup/tests/main.nf.test b/modules/nf-core/seqkit/rmdup/tests/main.nf.test index e990443f286..46556cf79be 100644 --- a/modules/nf-core/seqkit/rmdup/tests/main.nf.test +++ b/modules/nf-core/seqkit/rmdup/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) @@ -35,6 +36,7 @@ nextflow_process { when { process { """ + // testy mctestface def repeated_fasta = file('repeated.fasta') repeated_fasta.text = '>A\\nAGCTAGCTAGCT\\n>B\\nAGCTAGCTAGCT\\n>A\\nAGCTAGCTAGCT' @@ -60,6 +62,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true) @@ -82,6 +85,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) @@ -104,6 +108,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test_1' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) @@ -128,6 +133,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) @@ -153,6 +159,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'genome' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) diff --git a/modules/nf-core/seqkit/seq/tests/main.nf.test b/modules/nf-core/seqkit/seq/tests/main.nf.test index 9fd1c08583e..17f8b0313d9 100644 --- a/modules/nf-core/seqkit/seq/tests/main.nf.test +++ b/modules/nf-core/seqkit/seq/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) @@ -35,6 +36,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true) @@ -56,6 +58,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) @@ -77,6 +80,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test_1' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) @@ -101,6 +105,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) @@ -125,6 +130,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'genome' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) diff --git a/modules/nf-core/seqkit/sliding/tests/main.nf.test b/modules/nf-core/seqkit/sliding/tests/main.nf.test index ee24476ca7f..65b664dda18 100644 --- a/modules/nf-core/seqkit/sliding/tests/main.nf.test +++ b/modules/nf-core/seqkit/sliding/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] ] @@ -39,6 +40,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ] ] @@ -63,6 +65,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] ] diff --git a/modules/nf-core/seqkit/sort/tests/main.nf.test b/modules/nf-core/seqkit/sort/tests/main.nf.test index 467d50b063e..edf6ddbcb7d 100644 --- a/modules/nf-core/seqkit/sort/tests/main.nf.test +++ b/modules/nf-core/seqkit/sort/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) @@ -35,6 +36,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true) @@ -56,6 +58,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) @@ -77,6 +80,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test_1' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) @@ -101,6 +105,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) @@ -125,6 +130,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'genome' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) diff --git a/modules/nf-core/seqkit/split2/tests/main.nf.test b/modules/nf-core/seqkit/split2/tests/main.nf.test index ea48154b2c9..5285f9a1ce7 100644 --- a/modules/nf-core/seqkit/split2/tests/main.nf.test +++ b/modules/nf-core/seqkit/split2/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ] ] @@ -38,6 +39,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ] @@ -63,6 +65,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ] ] @@ -85,6 +88,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ] ] @@ -108,6 +112,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ] @@ -133,6 +138,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ] ] @@ -155,6 +161,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ] ] @@ -178,6 +185,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ] @@ -203,6 +211,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ] ] diff --git a/modules/nf-core/seqkit/stats/tests/main.nf.test b/modules/nf-core/seqkit/stats/tests/main.nf.test index 2cd4eb49e03..1c5859b3a97 100644 --- a/modules/nf-core/seqkit/stats/tests/main.nf.test +++ b/modules/nf-core/seqkit/stats/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [[ id:'test', single_end:true ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ] @@ -35,6 +36,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [[ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) @@ -57,6 +59,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [[ id:'test', single_end:true ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/nanopore/fastq/test.fastq.gz', checkIfExists: true) ] @@ -78,6 +81,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [[ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] @@ -99,6 +103,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [[ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/transcriptome.fasta', checkIfExists: true) ] @@ -122,6 +127,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [[ id:'test', single_end:true ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ] diff --git a/modules/nf-core/seqkit/tab2fx/tests/main.nf.test b/modules/nf-core/seqkit/tab2fx/tests/main.nf.test index b38cc82d278..fc9b0b9b888 100644 --- a/modules/nf-core/seqkit/tab2fx/tests/main.nf.test +++ b/modules/nf-core/seqkit/tab2fx/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.txt.zst', checkIfExists: true) ] ] @@ -35,6 +36,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.txt.zst', checkIfExists: true) ] ] @@ -56,6 +58,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.txt.zst', checkIfExists: true) ] ] @@ -77,6 +80,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.txt.zst', checkIfExists: true) ] ] @@ -100,6 +104,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.txt.zst', checkIfExists: true) ] ] diff --git a/modules/nf-core/seqsero2/tests/main.nf.test b/modules/nf-core/seqsero2/tests/main.nf.test index 457bec56a15..5065a4c024e 100644 --- a/modules/nf-core/seqsero2/tests/main.nf.test +++ b/modules/nf-core/seqsero2/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) diff --git a/modules/nf-core/seqtk/cutn/tests/main.nf.test b/modules/nf-core/seqtk/cutn/tests/main.nf.test index 46dfff1f894..60d09fd92d4 100644 --- a/modules/nf-core/seqtk/cutn/tests/main.nf.test +++ b/modules/nf-core/seqtk/cutn/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true) @@ -39,6 +40,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true) diff --git a/modules/nf-core/seqtk/mergepe/tests/main.nf.test b/modules/nf-core/seqtk/mergepe/tests/main.nf.test index b55ab3e626b..bc8e02051bf 100644 --- a/modules/nf-core/seqtk/mergepe/tests/main.nf.test +++ b/modules/nf-core/seqtk/mergepe/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) @@ -39,6 +40,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), @@ -66,6 +68,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) diff --git a/modules/nf-core/seqtk/rename/tests/main.nf.test b/modules/nf-core/seqtk/rename/tests/main.nf.test index 1ac2c3c3a24..67b21c2a0ae 100644 --- a/modules/nf-core/seqtk/rename/tests/main.nf.test +++ b/modules/nf-core/seqtk/rename/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) @@ -35,6 +36,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) @@ -57,6 +59,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) diff --git a/modules/nf-core/seqtk/sample/tests/main.nf.test b/modules/nf-core/seqtk/sample/tests/main.nf.test index c121c9d9820..453e61f9aff 100644 --- a/modules/nf-core/seqtk/sample/tests/main.nf.test +++ b/modules/nf-core/seqtk/sample/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), @@ -37,6 +38,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), @@ -60,6 +62,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), diff --git a/modules/nf-core/seqtk/seq/tests/main.nf.test b/modules/nf-core/seqtk/seq/tests/main.nf.test index 191bc13e1ef..14886a7bc3a 100644 --- a/modules/nf-core/seqtk/seq/tests/main.nf.test +++ b/modules/nf-core/seqtk/seq/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) @@ -37,6 +38,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) @@ -60,6 +62,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) diff --git a/modules/nf-core/seqtk/subseq/tests/main.nf.test b/modules/nf-core/seqtk/subseq/tests/main.nf.test index fa8fad692d8..25a15174241 100644 --- a/modules/nf-core/seqtk/subseq/tests/main.nf.test +++ b/modules/nf-core/seqtk/subseq/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) @@ -38,6 +39,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) diff --git a/modules/nf-core/sequenzautils/bam2seqz/tests/main.nf.test b/modules/nf-core/sequenzautils/bam2seqz/tests/main.nf.test index fbfb132164b..c4fde49d393 100644 --- a/modules/nf-core/sequenzautils/bam2seqz/tests/main.nf.test +++ b/modules/nf-core/sequenzautils/bam2seqz/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), @@ -41,6 +42,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), diff --git a/modules/nf-core/sequenzautils/gcwiggle/tests/main.nf.test b/modules/nf-core/sequenzautils/gcwiggle/tests/main.nf.test index 23a8eefc49d..3396c557fa4 100644 --- a/modules/nf-core/sequenzautils/gcwiggle/tests/main.nf.test +++ b/modules/nf-core/sequenzautils/gcwiggle/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] @@ -39,6 +40,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] diff --git a/modules/nf-core/seroba/run/tests/main.nf.test b/modules/nf-core/seroba/run/tests/main.nf.test index d45d1cc2a7d..22a23dbca2f 100644 --- a/modules/nf-core/seroba/run/tests/main.nf.test +++ b/modules/nf-core/seroba/run/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ diff --git a/modules/nf-core/severus/tests/main.nf.test b/modules/nf-core/severus/tests/main.nf.test index 1b85a109f04..56caba3be0c 100644 --- a/modules/nf-core/severus/tests/main.nf.test +++ b/modules/nf-core/severus/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test2.sorted.bam', checkIfExists: true), @@ -184,6 +185,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.phased.bam', checkIfExists: true), diff --git a/modules/nf-core/shasta/tests/main.nf.test b/modules/nf-core/shasta/tests/main.nf.test index ee6654930a7..84aa6a721d8 100644 --- a/modules/nf-core/shasta/tests/main.nf.test +++ b/modules/nf-core/shasta/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', model:'Nanopore-Dec2019' ], // meta map [ file(params.modules_testdata_base_path + 'genomics/prokaryotes/candidatus_portiera_aleyrodidarum/nanopore/fastq/test.fastq.gz', checkIfExists: true) ], diff --git a/modules/nf-core/shasum/tests/main.nf.test b/modules/nf-core/shasum/tests/main.nf.test index 91026a5d80f..57771200749 100644 --- a/modules/nf-core/shasum/tests/main.nf.test +++ b/modules/nf-core/shasum/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) diff --git a/modules/nf-core/shigatyper/tests/main.nf.test b/modules/nf-core/shigatyper/tests/main.nf.test index a08562e5288..46d8224f85e 100644 --- a/modules/nf-core/shigatyper/tests/main.nf.test +++ b/modules/nf-core/shigatyper/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false, is_ont:false ], // meta map [ @@ -39,6 +40,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true, is_ont:false ], // meta map [ @@ -63,6 +65,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true, is_ont:true ], // meta map [ @@ -89,6 +92,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true, is_ont:true ], // meta map [ diff --git a/modules/nf-core/shinyngs/app/tests/main.nf.test b/modules/nf-core/shinyngs/app/tests/main.nf.test index 39d6e27ecae..bd78b5a4c50 100644 --- a/modules/nf-core/shinyngs/app/tests/main.nf.test +++ b/modules/nf-core/shinyngs/app/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface expression_test_data_dir = params.modules_testdata_base_path + 'genomics/mus_musculus/rnaseq_expression/' expression_sample_sheet = file(expression_test_data_dir + 'SRP254919.samplesheet.csv', checkIfExists: true) @@ -58,6 +59,7 @@ nextflow_process { when { process { """ + // testy mctestface expression_test_data_dir = params.modules_testdata_base_path + 'genomics/mus_musculus/rnaseq_expression/' expression_sample_sheet = file(expression_test_data_dir + 'SRP254919.samplesheet.csv', checkIfExists: true) @@ -98,6 +100,7 @@ nextflow_process { when { process { """ + // testy mctestface expression_test_data_dir = params.modules_testdata_base_path + 'genomics/mus_musculus/rnaseq_expression/' expression_sample_sheet = file(expression_test_data_dir + 'SRP254919.samplesheet.csv', checkIfExists: true) diff --git a/modules/nf-core/shinyngs/staticexploratory/tests/main.nf.test b/modules/nf-core/shinyngs/staticexploratory/tests/main.nf.test index 3338aba1dfc..0e52b440e0d 100644 --- a/modules/nf-core/shinyngs/staticexploratory/tests/main.nf.test +++ b/modules/nf-core/shinyngs/staticexploratory/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface expression_test_data_dir = params.modules_testdata_base_path + 'genomics/mus_musculus/rnaseq_expression/' expression_sample_sheet = file(expression_test_data_dir + 'SRP254919.samplesheet.csv', checkIfExists: true) @@ -49,6 +50,7 @@ nextflow_process { when { process { """ + // testy mctestface expression_test_data_dir = params.modules_testdata_base_path + 'genomics/mus_musculus/rnaseq_expression/' expression_sample_sheet = file(expression_test_data_dir + 'SRP254919.samplesheet.csv', checkIfExists: true) @@ -84,6 +86,7 @@ nextflow_process { when { process { """ + // testy mctestface expression_test_data_dir = params.modules_testdata_base_path + 'genomics/mus_musculus/rnaseq_expression/' expression_sample_sheet = file(expression_test_data_dir + 'SRP254919.samplesheet.csv', checkIfExists: true) @@ -119,6 +122,7 @@ nextflow_process { when { process { """ + // testy mctestface expression_test_data_dir = params.modules_testdata_base_path + 'genomics/mus_musculus/rnaseq_expression/' expression_sample_sheet = file(expression_test_data_dir + 'SRP254919.samplesheet.csv', checkIfExists: true) diff --git a/modules/nf-core/shovill/tests/main.nf.test b/modules/nf-core/shovill/tests/main.nf.test index 1f3d0917d67..6af7f759586 100644 --- a/modules/nf-core/shovill/tests/main.nf.test +++ b/modules/nf-core/shovill/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ file("https://github.com/nf-core/test-datasets/raw/bacass/ERR044595_1M_1.fastq.gz", checkIfExists: true), file("https://github.com/nf-core/test-datasets/raw/bacass/ERR044595_1M_2.fastq.gz", checkIfExists: true) ] @@ -43,6 +44,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ] @@ -68,6 +70,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ] @@ -92,6 +95,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ] diff --git a/modules/nf-core/sickle/tests/main.nf.test b/modules/nf-core/sickle/tests/main.nf.test index 740420a09d8..5644e614a22 100644 --- a/modules/nf-core/sickle/tests/main.nf.test +++ b/modules/nf-core/sickle/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ], @@ -45,6 +46,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false, qual:'sanger' ], // meta map [ diff --git a/modules/nf-core/simpleaf/index/tests/main.nf.test b/modules/nf-core/simpleaf/index/tests/main.nf.test index f21e12fe61b..0b4fcfdc40d 100644 --- a/modules/nf-core/simpleaf/index/tests/main.nf.test +++ b/modules/nf-core/simpleaf/index/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface genome_fasta = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) gtf = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) meta = [ 'id': 'human_genome'] @@ -45,6 +46,7 @@ nextflow_process { when { process { """ + // testy mctestface transcriptome_fasta = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/transcriptome.fasta', checkIfExists: true) meta = [ 'id': 'human_transcriptome'] @@ -73,6 +75,7 @@ nextflow_process { when { process { """ + // testy mctestface transcriptome_fasta = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/transcriptome.fasta', checkIfExists: true) meta = [ 'id': 'human_transcriptome'] diff --git a/modules/nf-core/sistr/tests/main.nf.test b/modules/nf-core/sistr/tests/main.nf.test index f9a0edadae4..d55a2eb130a 100644 --- a/modules/nf-core/sistr/tests/main.nf.test +++ b/modules/nf-core/sistr/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/prokaryotes/haemophilus_influenzae/genome/genome.fna.gz', checkIfExists: true) diff --git a/modules/nf-core/slimfastq/tests/main.nf.test b/modules/nf-core/slimfastq/tests/main.nf.test index b2c47eec774..0d62cfb2bf2 100644 --- a/modules/nf-core/slimfastq/tests/main.nf.test +++ b/modules/nf-core/slimfastq/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) @@ -36,6 +37,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ @@ -61,6 +63,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/nanopore/fastq/test.fastq.gz', checkIfExists: true) @@ -83,6 +86,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/fastq/alz.ccs.fastq.gz', checkIfExists: true) diff --git a/modules/nf-core/smncopynumbercaller/tests/main.nf.test b/modules/nf-core/smncopynumbercaller/tests/main.nf.test index ce42bb04fbe..a69bed3d737 100644 --- a/modules/nf-core/smncopynumbercaller/tests/main.nf.test +++ b/modules/nf-core/smncopynumbercaller/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.chr6.bam', checkIfExists: true), @@ -38,6 +39,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.chr6.bam', checkIfExists: true), diff --git a/modules/nf-core/smoothxg/tests/main.nf.test b/modules/nf-core/smoothxg/tests/main.nf.test index 1a2ee9188dd..85262a811ea 100644 --- a/modules/nf-core/smoothxg/tests/main.nf.test +++ b/modules/nf-core/smoothxg/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/gfa/assembly.gfa', checkIfExists: true) @@ -36,6 +37,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'pangenomics/homo_sapiens/pangenome.seqwish.gfa', checkIfExists: true) diff --git a/modules/nf-core/smoove/call/tests/main.nf.test b/modules/nf-core/smoove/call/tests/main.nf.test index df9d3c1ddb2..20eb56a5809 100644 --- a/modules/nf-core/smoove/call/tests/main.nf.test +++ b/modules/nf-core/smoove/call/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), @@ -40,6 +41,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), @@ -68,6 +70,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), diff --git a/modules/nf-core/snakemake/tests/main.nf.test b/modules/nf-core/snakemake/tests/main.nf.test index 06205f0dea9..fc0b6511b54 100644 --- a/modules/nf-core/snakemake/tests/main.nf.test +++ b/modules/nf-core/snakemake/tests/main.nf.test @@ -12,6 +12,7 @@ nextflow_process { when { process { """ + // testy mctestface // Input file input[0] = [ [ id: 'input'], diff --git a/modules/nf-core/snapaligner/index/tests/main.nf.test b/modules/nf-core/snapaligner/index/tests/main.nf.test index ea72443ed19..3bef62a9cc7 100644 --- a/modules/nf-core/snapaligner/index/tests/main.nf.test +++ b/modules/nf-core/snapaligner/index/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id:"test"], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true), @@ -44,6 +45,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id:"test"], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true), diff --git a/modules/nf-core/sniffles/tests/main.nf.test b/modules/nf-core/sniffles/tests/main.nf.test index 9560b02d255..7da63a98b4e 100644 --- a/modules/nf-core/sniffles/tests/main.nf.test +++ b/modules/nf-core/sniffles/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam', checkIfExists: true), @@ -49,6 +50,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam', checkIfExists: true), @@ -82,6 +84,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam', checkIfExists: true), @@ -118,6 +121,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam', checkIfExists: true), @@ -159,6 +163,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam', checkIfExists: true), @@ -191,6 +196,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam', checkIfExists: true), @@ -223,6 +229,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam', checkIfExists: true), @@ -255,6 +262,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam', checkIfExists: true), diff --git a/modules/nf-core/snippy/run/tests/main.nf.test b/modules/nf-core/snippy/run/tests/main.nf.test index 25a39baa298..d01bf5def83 100644 --- a/modules/nf-core/snippy/run/tests/main.nf.test +++ b/modules/nf-core/snippy/run/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ diff --git a/modules/nf-core/snpdists/tests/main.nf.test b/modules/nf-core/snpdists/tests/main.nf.test index f1d7c7f608d..da713ebb802 100644 --- a/modules/nf-core/snpdists/tests/main.nf.test +++ b/modules/nf-core/snpdists/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/informative_sites.fas', checkIfExists: true) ] diff --git a/modules/nf-core/snpeff/download/tests/main.nf.test b/modules/nf-core/snpeff/download/tests/main.nf.test index ef547c6f2e9..320929d660a 100644 --- a/modules/nf-core/snpeff/download/tests/main.nf.test +++ b/modules/nf-core/snpeff/download/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:"WBcel235.105" ], "WBcel235.105" ] """ @@ -34,6 +35,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:"WBcel235.105" ], "WBcel235.105" ] """ diff --git a/modules/nf-core/snpeff/snpeff/tests/main.nf.test b/modules/nf-core/snpeff/snpeff/tests/main.nf.test index 2be0b7d72c7..588c28c8349 100644 --- a/modules/nf-core/snpeff/snpeff/tests/main.nf.test +++ b/modules/nf-core/snpeff/snpeff/tests/main.nf.test @@ -27,6 +27,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) diff --git a/modules/nf-core/snpsift/annotate/tests/main.nf.test b/modules/nf-core/snpsift/annotate/tests/main.nf.test index f024994e4aa..8918e58ed3a 100644 --- a/modules/nf-core/snpsift/annotate/tests/main.nf.test +++ b/modules/nf-core/snpsift/annotate/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), @@ -47,6 +48,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'tester', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true), @@ -79,6 +81,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'tester', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true), diff --git a/modules/nf-core/snpsift/dbnsfp/tests/main.nf.test b/modules/nf-core/snpsift/dbnsfp/tests/main.nf.test index 1c411ef9ef1..39f172b1e17 100644 --- a/modules/nf-core/snpsift/dbnsfp/tests/main.nf.test +++ b/modules/nf-core/snpsift/dbnsfp/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/test.genome_21.somatic_sv.vcf.gz', checkIfExists: true), @@ -48,6 +49,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'tester', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/test.genome_21.somatic_sv.vcf.gz', checkIfExists: true), @@ -80,6 +82,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'tester', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/test.genome_21.somatic_sv.vcf.gz', checkIfExists: true), diff --git a/modules/nf-core/snpsift/split/tests/main.nf.test b/modules/nf-core/snpsift/split/tests/main.nf.test index c1495794097..214af6cda2c 100644 --- a/modules/nf-core/snpsift/split/tests/main.nf.test +++ b/modules/nf-core/snpsift/split/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', split:true], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/test.rnaseq.vcf', checkIfExists: true) @@ -41,6 +42,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', split:true ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true) @@ -67,6 +69,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', split:false ], // meta map [ diff --git a/modules/nf-core/snpsites/tests/main.nf.test b/modules/nf-core/snpsites/tests/main.nf.test index 60ae4b9a7f7..f5ac3f9aee0 100644 --- a/modules/nf-core/snpsites/tests/main.nf.test +++ b/modules/nf-core/snpsites/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/all_sites.fas', checkIfExists: true) """ } @@ -32,6 +33,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/all_sites.fas', checkIfExists: true) """ } diff --git a/modules/nf-core/somalier/extract/tests/main.nf.test b/modules/nf-core/somalier/extract/tests/main.nf.test index dfc7e8a5d6b..a01a24719bd 100644 --- a/modules/nf-core/somalier/extract/tests/main.nf.test +++ b/modules/nf-core/somalier/extract/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam', checkIfExists: true), @@ -51,6 +52,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam', checkIfExists: true), diff --git a/modules/nf-core/somalier/relate/tests/main.nf.test b/modules/nf-core/somalier/relate/tests/main.nf.test index 5f17456d399..033a1322320 100644 --- a/modules/nf-core/somalier/relate/tests/main.nf.test +++ b/modules/nf-core/somalier/relate/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'cohort', single_end:false ], // meta map [ @@ -41,6 +42,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'cohort', single_end:false ], // meta map [ @@ -70,6 +72,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'cohort', single_end:false ], // meta map [ @@ -99,6 +102,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'cohort', single_end:false ], // meta map [ diff --git a/modules/nf-core/sortmerna/tests/main.nf.test b/modules/nf-core/sortmerna/tests/main.nf.test index 73bc1195032..33a3944be7e 100644 --- a/modules/nf-core/sortmerna/tests/main.nf.test +++ b/modules/nf-core/sortmerna/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([[],[]]) input[1] = [ [id:'test2'], // meta map [ file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.fasta", checkIfExists: true) ] @@ -42,6 +43,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([[],[]]) input[1] = [ [id:'test2'], // meta map [ file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.fasta", checkIfExists: true) ] @@ -67,6 +69,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true) ] ] @@ -106,6 +109,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true) ] ] @@ -141,6 +145,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ @@ -184,6 +189,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true), @@ -240,6 +246,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true) ] ] @@ -295,6 +302,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true) ] ] diff --git a/modules/nf-core/sourmash/compare/tests/main.nf.test b/modules/nf-core/sourmash/compare/tests/main.nf.test index 43963e58faf..883f3786ac8 100644 --- a/modules/nf-core/sourmash/compare/tests/main.nf.test +++ b/modules/nf-core/sourmash/compare/tests/main.nf.test @@ -37,6 +37,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = SOURMASH_SKETCH.out.signatures.collect{ it[1] }.map { it -> [ [id: "group1" ], it ] } input[1] = [] input[2] = true // save_numpy_matrix @@ -61,6 +62,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = SOURMASH_SKETCH.out.signatures.collect{ it[1] }.map { it -> [ [id: "group1" ], it ] } input[1] = [] input[2] = true // save_numpy_matrix diff --git a/modules/nf-core/sourmash/index/tests/main.nf.test b/modules/nf-core/sourmash/index/tests/main.nf.test index 2213410bb2d..be8aac3ff86 100644 --- a/modules/nf-core/sourmash/index/tests/main.nf.test +++ b/modules/nf-core/sourmash/index/tests/main.nf.test @@ -29,6 +29,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = SOURMASH_SKETCH.out.signatures input[1] = 31 """ @@ -53,6 +54,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = SOURMASH_SKETCH.out.signatures input[1] = 31 """ diff --git a/modules/nf-core/spaceranger/count/tests/main.nf.test b/modules/nf-core/spaceranger/count/tests/main.nf.test index 2be65252513..0f215c5e4d8 100644 --- a/modules/nf-core/spaceranger/count/tests/main.nf.test +++ b/modules/nf-core/spaceranger/count/tests/main.nf.test @@ -41,6 +41,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id: 'Visium_FFPE_Human_Ovarian_Cancer', @@ -118,6 +119,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id: 'Visium_FFPE_Human_Ovarian_Cancer', @@ -177,6 +179,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id: 'CytAssist_11mm_FFPE_Human_Glioblastoma_2', diff --git a/modules/nf-core/spaceranger/mkgtf/tests/main.nf.test b/modules/nf-core/spaceranger/mkgtf/tests/main.nf.test index cbabc09b107..d4076e0d61b 100644 --- a/modules/nf-core/spaceranger/mkgtf/tests/main.nf.test +++ b/modules/nf-core/spaceranger/mkgtf/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] diff --git a/modules/nf-core/spaceranger/mkref/tests/main.nf.test b/modules/nf-core/spaceranger/mkref/tests/main.nf.test index eb710c72759..9a9b2eaf398 100644 --- a/modules/nf-core/spaceranger/mkref/tests/main.nf.test +++ b/modules/nf-core/spaceranger/mkref/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) input[2] = 'homo_sapiens_chr22_reference' diff --git a/modules/nf-core/spades/tests/main.nf.test b/modules/nf-core/spades/tests/main.nf.test index 3a93f48680c..8fad32556ae 100644 --- a/modules/nf-core/spades/tests/main.nf.test +++ b/modules/nf-core/spades/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_2.fastq.gz", checkIfExists: true) ], [], @@ -43,6 +44,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true), file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_2.fastq.gz", checkIfExists: true) ], @@ -76,6 +78,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true), file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_2.fastq.gz", checkIfExists: true) ], @@ -109,6 +112,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true), file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_2.fastq.gz", checkIfExists: true) ], @@ -141,6 +145,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true), file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_2.fastq.gz", checkIfExists: true) ], @@ -173,6 +178,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ file("https://github.com/nf-core/test-datasets/raw/viralrecon/illumina/sispa/SRR11140744_R1.fastq.gz", checkIfExists: true), file("https://github.com/nf-core/test-datasets/raw/viralrecon/illumina/sispa/SRR11140744_R2.fastq.gz", checkIfExists: true) ], @@ -205,6 +211,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true), file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_2.fastq.gz", checkIfExists: true) ], diff --git a/modules/nf-core/splitubam/tests/main.nf.test b/modules/nf-core/splitubam/tests/main.nf.test index 270df28b634..b09c5caf933 100644 --- a/modules/nf-core/splitubam/tests/main.nf.test +++ b/modules/nf-core/splitubam/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) @@ -47,6 +48,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) diff --git a/modules/nf-core/spotiflow/tests/main.nf.test b/modules/nf-core/spotiflow/tests/main.nf.test index 03203caa16c..425a0cd0219 100644 --- a/modules/nf-core/spotiflow/tests/main.nf.test +++ b/modules/nf-core/spotiflow/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test_img'], file(params.modules_testdata_base_path + 'imaging/spot_detection/immunofluorescence.tif', checkIfExists: true) @@ -37,6 +38,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], diff --git a/modules/nf-core/spring/compress/tests/main.nf.test b/modules/nf-core/spring/compress/tests/main.nf.test index 45690c34fd6..38e7d6290bb 100644 --- a/modules/nf-core/spring/compress/tests/main.nf.test +++ b/modules/nf-core/spring/compress/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), @@ -42,6 +43,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), diff --git a/modules/nf-core/spring/decompress/test/main.nf.test b/modules/nf-core/spring/decompress/test/main.nf.test index 550c6746b82..f50973e97d5 100644 --- a/modules/nf-core/spring/decompress/test/main.nf.test +++ b/modules/nf-core/spring/decompress/test/main.nf.test @@ -28,6 +28,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = SPRING_COMPRESS.out.spring input[1] = true // write_one_fastq_gz """ @@ -62,6 +63,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = SPRING_COMPRESS.out.spring input[1] = false // write_one_fastq_gz """ diff --git a/modules/nf-core/sratools/fasterqdump/tests/main.nf.test b/modules/nf-core/sratools/fasterqdump/tests/main.nf.test index 6996cd18a14..1efef0aabc8 100644 --- a/modules/nf-core/sratools/fasterqdump/tests/main.nf.test +++ b/modules/nf-core/sratools/fasterqdump/tests/main.nf.test @@ -24,6 +24,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = UNTAR.out.untar.map{ meta, files -> [ [ id:'test_single_end', single_end:true ], files]} input[1] = file(params.modules_testdata_base_path + 'generic/config/ncbi_user_settings.mkfg', checkIfExists: true) input[2] = [] @@ -55,6 +56,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = UNTAR.out.untar.map{ meta, files -> [ [ id:'test_paired_end', single_end:false ], files]} input[1] = file(params.modules_testdata_base_path + 'generic/config/ncbi_user_settings.mkfg', checkIfExists: true) input[2] = [] @@ -77,6 +79,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test_single_end', single_end:true ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/sra/SRR13255544.tar.gz', checkIfExists: true) @@ -102,6 +105,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test_paired_end', single_end:false ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/sra/SRR11140744.tar.gz', checkIfExists: true) diff --git a/modules/nf-core/sratools/prefetch/tests/main.nf.test b/modules/nf-core/sratools/prefetch/tests/main.nf.test index 92034d40fce..67b34a74013 100644 --- a/modules/nf-core/sratools/prefetch/tests/main.nf.test +++ b/modules/nf-core/sratools/prefetch/tests/main.nf.test @@ -12,6 +12,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], 'DRR000774' ]) input[1] = file(params.modules_testdata_base_path + 'generic/config/ncbi_user_settings.mkfg', checkIfExists: true) input[2] = [] @@ -32,6 +33,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], 'SRR1170046' ]) input[1] = file(params.modules_testdata_base_path + 'generic/config/ncbi_user_settings.mkfg', checkIfExists: true) input[2] = [] @@ -54,6 +56,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], 'DRR000774' ]) input[1] = file(params.modules_testdata_base_path + 'generic/config/ncbi_user_settings.mkfg', checkIfExists: true) input[2] = [] diff --git a/modules/nf-core/ssuissero/tests/main.nf.test b/modules/nf-core/ssuissero/tests/main.nf.test index e8e68a20573..7991876f679 100644 --- a/modules/nf-core/ssuissero/tests/main.nf.test +++ b/modules/nf-core/ssuissero/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/prokaryotes/haemophilus_influenzae/genome/genome.fna.gz', checkIfExists: true) diff --git a/modules/nf-core/stadeniolib/scramble/tests/main.nf.test b/modules/nf-core/stadeniolib/scramble/tests/main.nf.test index 1534cd776e9..0c4a4fec28d 100644 --- a/modules/nf-core/stadeniolib/scramble/tests/main.nf.test +++ b/modules/nf-core/stadeniolib/scramble/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) @@ -46,6 +47,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) diff --git a/modules/nf-core/staphopiasccmec/tests/main.nf.test b/modules/nf-core/staphopiasccmec/tests/main.nf.test index e500c446232..c2b2e9d737e 100644 --- a/modules/nf-core/staphopiasccmec/tests/main.nf.test +++ b/modules/nf-core/staphopiasccmec/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) @@ -37,6 +38,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) diff --git a/modules/nf-core/star/align/tests/main.nf.test b/modules/nf-core/star/align/tests/main.nf.test index 2d9f72ddc15..b0d469fcaa7 100644 --- a/modules/nf-core/star/align/tests/main.nf.test +++ b/modules/nf-core/star/align/tests/main.nf.test @@ -33,6 +33,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:true ], // meta map [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true) ] @@ -98,6 +99,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map [ @@ -166,6 +168,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map [ @@ -234,6 +237,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map [ @@ -302,6 +306,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map [ @@ -373,6 +378,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:true ], // meta map [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true) ] @@ -422,6 +428,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map [ @@ -474,6 +481,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map [ @@ -526,6 +534,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map [ @@ -578,6 +587,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map [ diff --git a/modules/nf-core/star/genomegenerate/tests/main.nf.test b/modules/nf-core/star/genomegenerate/tests/main.nf.test index 4d619c47351..ce10ac1affd 100644 --- a/modules/nf-core/star/genomegenerate/tests/main.nf.test +++ b/modules/nf-core/star/genomegenerate/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test_fasta' ], [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] @@ -41,6 +42,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test_fasta' ], [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] @@ -68,6 +70,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test_fasta' ], [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] @@ -95,6 +98,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test_fasta' ], [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] diff --git a/modules/nf-core/star/starsolo/tests/main.nf.test b/modules/nf-core/star/starsolo/tests/main.nf.test index e10107da96f..3e4230ff9fd 100644 --- a/modules/nf-core/star/starsolo/tests/main.nf.test +++ b/modules/nf-core/star/starsolo/tests/main.nf.test @@ -33,6 +33,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', umi_len:'12' ], 'CB_UMI_Simple', @@ -88,6 +89,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', umi_len:'12' ], 'CB_UMI_Simple', diff --git a/modules/nf-core/staramr/search/tests/main.nf.test b/modules/nf-core/staramr/search/tests/main.nf.test index fa72c63b776..bd4f53198df 100644 --- a/modules/nf-core/staramr/search/tests/main.nf.test +++ b/modules/nf-core/staramr/search/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/genome/genome.fna.gz', checkIfExists: true) diff --git a/modules/nf-core/stardist/tests/main.nf.test b/modules/nf-core/stardist/tests/main.nf.test index c511ee6dcb6..f592593a8e4 100644 --- a/modules/nf-core/stardist/tests/main.nf.test +++ b/modules/nf-core/stardist/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'imaging/segmentation/nuclear_image.tif', checkIfExists: true) @@ -37,6 +38,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'imaging/segmentation/nuclear_image.tif', checkIfExists: true) diff --git a/modules/nf-core/stranger/tests/main.nf.test b/modules/nf-core/stranger/tests/main.nf.test index 13c61f43fb2..8cac63637e1 100644 --- a/modules/nf-core/stranger/tests/main.nf.test +++ b/modules/nf-core/stranger/tests/main.nf.test @@ -42,6 +42,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = EXPANSIONHUNTER.out.vcf input[1] = [ [id:'catalogue'], @@ -65,6 +66,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = EXPANSIONHUNTER.out.vcf input[1] = [ [id:'catalogue'], diff --git a/modules/nf-core/strelka/germline/tests/main.nf.test b/modules/nf-core/strelka/germline/tests/main.nf.test index e2be9e18306..c8095364082 100644 --- a/modules/nf-core/strelka/germline/tests/main.nf.test +++ b/modules/nf-core/strelka/germline/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram.crai', checkIfExists: true), @@ -41,6 +42,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram.crai', checkIfExists: true), @@ -71,6 +73,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram.crai', checkIfExists: true), diff --git a/modules/nf-core/strelka/somatic/tests/main.nf.test b/modules/nf-core/strelka/somatic/tests/main.nf.test index 2203e6eea4b..c3a3410a638 100644 --- a/modules/nf-core/strelka/somatic/tests/main.nf.test +++ b/modules/nf-core/strelka/somatic/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram.crai', checkIfExists: true), @@ -45,6 +46,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram.crai', checkIfExists: true), @@ -79,6 +81,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram.crai', checkIfExists: true), diff --git a/modules/nf-core/stringtie/merge/tests/main.nf.test b/modules/nf-core/stringtie/merge/tests/main.nf.test index bcc648bc76f..c8abb5a4f3b 100644 --- a/modules/nf-core/stringtie/merge/tests/main.nf.test +++ b/modules/nf-core/stringtie/merge/tests/main.nf.test @@ -29,6 +29,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = STRINGTIE_STRINGTIE.out.transcript_gtf.map { it -> it[1] } input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) """ @@ -49,6 +50,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = STRINGTIE_STRINGTIE.out.transcript_gtf.map { it -> it[1] } input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) """ diff --git a/modules/nf-core/stringtie/stringtie/tests/main.nf.test b/modules/nf-core/stringtie/stringtie/tests/main.nf.test index 2204e849f38..dbed9a9b49a 100644 --- a/modules/nf-core/stringtie/stringtie/tests/main.nf.test +++ b/modules/nf-core/stringtie/stringtie/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', strandedness:'forward' ], // meta map [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true) ] @@ -40,6 +41,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', strandedness:'forward' ], // meta map [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true) ] @@ -67,6 +69,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', strandedness:'reverse' ], // meta map [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true) ] @@ -93,6 +96,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', strandedness:'reverse' ], // meta map [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true) ] @@ -122,6 +126,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', strandedness:'forward' ], // meta map [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true) ] @@ -146,6 +151,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', strandedness:'forward' ], // meta map [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true) ] @@ -170,6 +176,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', strandedness:'reverse' ], // meta map [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true) ] @@ -194,6 +201,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', strandedness:'reverse' ], // meta map [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true) ] diff --git a/modules/nf-core/subread/featurecounts/tests/main.nf.test b/modules/nf-core/subread/featurecounts/tests/main.nf.test index 3b95da33f67..69fdefa3fe4 100644 --- a/modules/nf-core/subread/featurecounts/tests/main.nf.test +++ b/modules/nf-core/subread/featurecounts/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true, strandedness:'forward' ], // meta map file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.single_end.bam", checkIfExists: true), @@ -40,6 +41,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true, strandedness:'forward' ], // meta map file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.single_end.bam", checkIfExists: true), @@ -62,6 +64,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true, strandedness:'reverse' ], // meta map file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.single_end.bam", checkIfExists: true), @@ -88,6 +91,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true, strandedness:'reverse' ], // meta map file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.single_end.bam", checkIfExists: true), @@ -110,6 +114,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true, strandedness:'unstranded' ], // meta map file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.single_end.bam", checkIfExists: true), @@ -136,6 +141,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true, strandedness:'unstranded' ], // meta map file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.single_end.bam", checkIfExists: true), diff --git a/modules/nf-core/summarizedexperiment/summarizedexperiment/tests/main.nf.test b/modules/nf-core/summarizedexperiment/summarizedexperiment/tests/main.nf.test index b51a76cda3c..9d087034f12 100644 --- a/modules/nf-core/summarizedexperiment/summarizedexperiment/tests/main.nf.test +++ b/modules/nf-core/summarizedexperiment/summarizedexperiment/tests/main.nf.test @@ -60,6 +60,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = TXIMETA_TXIMPORT.out.counts_gene.join(TXIMETA_TXIMPORT.out.tpm_gene).map{tuple(it[0], [it[1], it[2]])} input[1] = CUSTOM_TX2GENE.out.tx2gene input[2] = [ @@ -89,6 +90,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = TXIMETA_TXIMPORT.out.counts_gene.join(TXIMETA_TXIMPORT.out.tpm_gene).map{tuple(it[0], [it[1], it[2]])} input[1] = CUSTOM_TX2GENE.out.tx2gene input[2] = Channel.of([ [], [] ]) @@ -115,6 +117,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = TXIMETA_TXIMPORT.out.counts_gene.join(TXIMETA_TXIMPORT.out.tpm_gene).map{tuple(it[0], [it[1], it[2]])} input[1] = Channel.of([ [], [] ]) input[2] = Channel.of([ [], [] ]) @@ -141,6 +144,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = TXIMETA_TXIMPORT.out.counts_gene input[1] = Channel.of([ [], [] ]) input[2] = Channel.of([ [], [] ]) @@ -168,6 +172,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = TXIMETA_TXIMPORT.out.counts_gene.join(TXIMETA_TXIMPORT.out.tpm_gene).map{tuple(it[0], [it[1], it[2]])} input[1] = CUSTOM_TX2GENE.out.tx2gene input[2] = [ @@ -195,6 +200,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = TXIMETA_TXIMPORT.out.counts_gene.join(TXIMETA_TXIMPORT.out.tpm_gene).map{tuple(it[0], [it[1], it[2]])} input[1] = CUSTOM_TX2GENE.out.tx2gene input[2] = Channel.of([ [], [] ]) @@ -219,6 +225,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = TXIMETA_TXIMPORT.out.counts_gene.join(TXIMETA_TXIMPORT.out.tpm_gene).map{tuple(it[0], [it[1], it[2]])} input[1] = Channel.of([ [], [] ]) input[2] = Channel.of([ [], [] ]) @@ -243,6 +250,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = TXIMETA_TXIMPORT.out.counts_gene input[1] = Channel.of([ [], [] ]) input[2] = Channel.of([ [], [] ]) diff --git a/modules/nf-core/survivor/bedpetovcf/tests/main.nf.test b/modules/nf-core/survivor/bedpetovcf/tests/main.nf.test index 58be3136fd1..61e2d49554f 100644 --- a/modules/nf-core/survivor/bedpetovcf/tests/main.nf.test +++ b/modules/nf-core/survivor/bedpetovcf/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bedpe', checkIfExists: true) @@ -39,6 +40,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bedpe', checkIfExists: true) diff --git a/modules/nf-core/survivor/merge/tests/main.nf.test b/modules/nf-core/survivor/merge/tests/main.nf.test index 6ec81edeb41..4556705ff47 100644 --- a/modules/nf-core/survivor/merge/tests/main.nf.test +++ b/modules/nf-core/survivor/merge/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ @@ -50,6 +51,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ diff --git a/modules/nf-core/survivor/stats/tests/main.nf.test b/modules/nf-core/survivor/stats/tests/main.nf.test index d725a17f5ff..8edaf8c9f78 100644 --- a/modules/nf-core/survivor/stats/tests/main.nf.test +++ b/modules/nf-core/survivor/stats/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.vcf.gz', checkIfExists: true) @@ -45,6 +46,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz', checkIfExists: true) diff --git a/modules/nf-core/svdb/build/tests/main.nf.test b/modules/nf-core/svdb/build/tests/main.nf.test index ccf18f2b28b..d260e54fd4f 100644 --- a/modules/nf-core/svdb/build/tests/main.nf.test +++ b/modules/nf-core/svdb/build/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test' ], // meta map [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/sv_query.vcf.gz', checkIfExists: true) ] ]) @@ -37,6 +38,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test' ], // meta map [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/sv_query.vcf.gz', checkIfExists: true), @@ -66,6 +68,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test' ], // meta map [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/sv_query.vcf.gz', checkIfExists: true) ] ]) @@ -89,6 +92,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test' ], // meta map [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/sv_query.vcf.gz', checkIfExists: true), diff --git a/modules/nf-core/svdb/merge/tests/main.nf.test b/modules/nf-core/svdb/merge/tests/main.nf.test index 42f7c570677..68944b156e5 100644 --- a/modules/nf-core/svdb/merge/tests/main.nf.test +++ b/modules/nf-core/svdb/merge/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test' ], // meta map [file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true), @@ -37,6 +38,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test' ], // meta map [file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true), diff --git a/modules/nf-core/svdb/query/tests/main.nf.test b/modules/nf-core/svdb/query/tests/main.nf.test index 72e829158c6..7de59b10050 100644 --- a/modules/nf-core/svdb/query/tests/main.nf.test +++ b/modules/nf-core/svdb/query/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test' ], // meta map [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/sv_query.vcf.gz', checkIfExists: true) ] ]) diff --git a/modules/nf-core/svtk/countsvtypes/tests/main.nf.test b/modules/nf-core/svtk/countsvtypes/tests/main.nf.test index dedf25c7149..62b1b797e28 100644 --- a/modules/nf-core/svtk/countsvtypes/tests/main.nf.test +++ b/modules/nf-core/svtk/countsvtypes/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz', checkIfExists: true) diff --git a/modules/nf-core/svtyper/svtyper/tests/main.nf.test b/modules/nf-core/svtyper/svtyper/tests/main.nf.test index 8f9911fc268..da04fff4eef 100644 --- a/modules/nf-core/svtyper/svtyper/tests/main.nf.test +++ b/modules/nf-core/svtyper/svtyper/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), @@ -53,6 +54,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), diff --git a/modules/nf-core/svtyper/svtypersso/tests/main.nf.test b/modules/nf-core/svtyper/svtypersso/tests/main.nf.test index b263f3be7f0..95fd96134f3 100644 --- a/modules/nf-core/svtyper/svtypersso/tests/main.nf.test +++ b/modules/nf-core/svtyper/svtypersso/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), @@ -45,6 +46,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), @@ -72,6 +74,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), @@ -104,6 +107,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), diff --git a/modules/nf-core/svync/tests/main.nf.test b/modules/nf-core/svync/tests/main.nf.test index cba224c4c09..d6f5a2323a6 100644 --- a/modules/nf-core/svync/tests/main.nf.test +++ b/modules/nf-core/svync/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface vcf = Channel.of([ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/chr21/simulated_sv.vcf.gz', checkIfExists: true), @@ -61,6 +62,7 @@ nextflow_process { when { process { """ + // testy mctestface vcf = Channel.of([ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/chr21/simulated_sv.vcf.gz', checkIfExists: true), diff --git a/modules/nf-core/tabix/bgzip/tests/main.nf.test b/modules/nf-core/tabix/bgzip/tests/main.nf.test index d784aa07078..e0638d559cb 100644 --- a/modules/nf-core/tabix/bgzip/tests/main.nf.test +++ b/modules/nf-core/tabix/bgzip/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'bgzip_test' ], [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) ] @@ -37,6 +38,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'bedgz_test' ], [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed.gz', checkIfExists: true) ] @@ -64,6 +66,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:"test_stub" ], [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) ] @@ -89,6 +92,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:"gzi_compress_test" ], [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) ] diff --git a/modules/nf-core/tabix/bgziptabix/tests/main.nf.test b/modules/nf-core/tabix/bgziptabix/tests/main.nf.test index 4d4130dc07d..1feb853c605 100644 --- a/modules/nf-core/tabix/bgziptabix/tests/main.nf.test +++ b/modules/nf-core/tabix/bgziptabix/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'tbi_test' ], [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) ] @@ -41,6 +42,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'csi_test' ], [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) ] @@ -70,6 +72,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) ] @@ -99,6 +102,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) ] diff --git a/modules/nf-core/tabix/tabix/tests/main.nf.test b/modules/nf-core/tabix/tabix/tests/main.nf.test index 102b0d7bf38..c492e0ececd 100644 --- a/modules/nf-core/tabix/tabix/tests/main.nf.test +++ b/modules/nf-core/tabix/tabix/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'tbi_bed' ], [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed.gz', checkIfExists: true) ] @@ -38,6 +39,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'tbi_gff' ], [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gff3.gz', checkIfExists: true) ] @@ -62,6 +64,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'tbi_vcf' ], [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true) ] @@ -87,6 +90,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'vcf_csi' ], [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true) ] @@ -113,6 +117,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'vcf_csi_stub' ], [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true) ] diff --git a/modules/nf-core/tailfindr/tests/main.nf.test b/modules/nf-core/tailfindr/tests/main.nf.test index 55ec9412b2b..ff6cc5438c0 100644 --- a/modules/nf-core/tailfindr/tests/main.nf.test +++ b/modules/nf-core/tailfindr/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id: 'test' ], // meta map file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/tailfindr/test.fast5', checkIfExists: true) diff --git a/modules/nf-core/taxonkit/name2taxid/tests/main.nf.test b/modules/nf-core/taxonkit/name2taxid/tests/main.nf.test index 17ed24d9202..91d596ee2ed 100644 --- a/modules/nf-core/taxonkit/name2taxid/tests/main.nf.test +++ b/modules/nf-core/taxonkit/name2taxid/tests/main.nf.test @@ -29,6 +29,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map "SARS-CoV-2", @@ -53,6 +54,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of( [ [ id:'test', single_end:false ], // meta map '' @@ -78,6 +80,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map "SARS-CoV-2", diff --git a/modules/nf-core/taxpasta/merge/tests/main.nf.test b/modules/nf-core/taxpasta/merge/tests/main.nf.test index 886e93b9ccd..bdd2a0a0d63 100644 --- a/modules/nf-core/taxpasta/merge/tests/main.nf.test +++ b/modules/nf-core/taxpasta/merge/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface ch_test1_kraken = Channel.fromPath(params.modules_testdata_base_path + 'genomics/sarscov2/metagenome/test_1.kraken2.report.txt', checkIfExists: true).collectFile(name: 'test_1.kraken2.report.txt') ch_test2_kraken = Channel.fromPath(params.modules_testdata_base_path + 'genomics/sarscov2/metagenome/test_1.kraken2.report.txt', checkIfExists: true).collectFile(name: 'test_2.kraken2.report.txt') @@ -50,6 +51,7 @@ nextflow_process { when { process { """ + // testy mctestface ch_test1_kraken = Channel.fromPath(params.modules_testdata_base_path + 'genomics/sarscov2/metagenome/test_1.kraken2.report.txt', checkIfExists: true).collectFile(name: 'test_1.kraken2.report.txt') ch_test2_kraken = Channel.fromPath(params.modules_testdata_base_path + 'genomics/sarscov2/metagenome/test_1.kraken2.report.txt', checkIfExists: true).collectFile(name: 'test_2.kraken2.report.txt') @@ -90,6 +92,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [[id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/metagenome/test_1.kraken2.report.txt', checkIfExists: true)] input[1] = 'kraken2' input[2] = 'tsv' diff --git a/modules/nf-core/taxpasta/standardise/tests/main.nf.test b/modules/nf-core/taxpasta/standardise/tests/main.nf.test index e06ca7d609d..7bee26b6f96 100644 --- a/modules/nf-core/taxpasta/standardise/tests/main.nf.test +++ b/modules/nf-core/taxpasta/standardise/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [[id: 'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/metagenome/test_1.kraken2.report.txt', checkIfExists: true)] input[1] = "kraken2" input[2] = 'tsv' @@ -38,6 +39,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [[id: 'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/metagenome/test_1.kraken2.report.txt', checkIfExists: true)] input[1] = "kraken2" input[2] = 'tsv' diff --git a/modules/nf-core/tbprofiler/profile/tests/main.nf.test b/modules/nf-core/tbprofiler/profile/tests/main.nf.test index 6bd9c8b87b8..2dda1017e23 100644 --- a/modules/nf-core/tbprofiler/profile/tests/main.nf.test +++ b/modules/nf-core/tbprofiler/profile/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ @@ -50,6 +51,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/nanopore/fastq/test.fastq.gz', checkIfExists: true) diff --git a/modules/nf-core/tcoffee/align/tests/main.nf.test b/modules/nf-core/tcoffee/align/tests/main.nf.test index f0b1752ca8f..b9aae264d40 100644 --- a/modules/nf-core/tcoffee/align/tests/main.nf.test +++ b/modules/nf-core/tcoffee/align/tests/main.nf.test @@ -18,6 +18,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true) ] @@ -44,6 +45,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true) ] @@ -85,6 +87,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true) ] @@ -127,6 +130,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true) ] @@ -155,6 +159,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true) ] @@ -182,6 +187,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true) ] diff --git a/modules/nf-core/tcoffee/alncompare/tests/main.nf.test b/modules/nf-core/tcoffee/alncompare/tests/main.nf.test index 66e5f204cbd..daa8142ac76 100644 --- a/modules/nf-core/tcoffee/alncompare/tests/main.nf.test +++ b/modules/nf-core/tcoffee/alncompare/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true), @@ -37,6 +38,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true), diff --git a/modules/nf-core/tcoffee/consensus/tests/main.nf.test b/modules/nf-core/tcoffee/consensus/tests/main.nf.test index 5f013e3f9e7..3cc13d18eef 100644 --- a/modules/nf-core/tcoffee/consensus/tests/main.nf.test +++ b/modules/nf-core/tcoffee/consensus/tests/main.nf.test @@ -59,6 +59,7 @@ nextflow_process { when { process { """ + // testy mctestface msas = FAMSA_ALIGN.out.alignment.mix(MAGUS_ALIGN.out.alignment).groupTuple() input[0] = msas input[1] = [[:],[]] @@ -80,6 +81,7 @@ nextflow_process { when { process { """ + // testy mctestface msas = FAMSA_ALIGN.out.alignment.mix(MAGUS_ALIGN.out.alignment).groupTuple() input[0] = msas input[1] = CLUSTALO_GUIDETREE.out.tree.collect{ meta, tree -> tree }.map{ tree -> [[ id: 'test'], tree]} @@ -103,6 +105,7 @@ nextflow_process { when { process { """ + // testy mctestface msas = FAMSA_ALIGN.out.alignment.mix(MAGUS_ALIGN.out.alignment).groupTuple() input[0] = msas input[1] = [[:],[]] diff --git a/modules/nf-core/tcoffee/irmsd/tests/main.nf.test b/modules/nf-core/tcoffee/irmsd/tests/main.nf.test index dfb68629535..2086fb1c7a4 100644 --- a/modules/nf-core/tcoffee/irmsd/tests/main.nf.test +++ b/modules/nf-core/tcoffee/irmsd/tests/main.nf.test @@ -42,6 +42,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin.ref", checkIfExists: true) @@ -66,6 +67,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = PIGZ_COMPRESS.out.archive input[1] = UNTAR.out.untar.map { meta,dir -> [[ id:'test' ], file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/templates/seatoxin-ref_template.txt", checkIfExists: true) ,file(dir).listFiles().collect()]} """ @@ -89,6 +91,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin.ref", checkIfExists: true) diff --git a/modules/nf-core/tcoffee/seqreformat/tests/main.nf.test b/modules/nf-core/tcoffee/seqreformat/tests/main.nf.test index 1510e92075b..0b96ae5be85 100644 --- a/modules/nf-core/tcoffee/seqreformat/tests/main.nf.test +++ b/modules/nf-core/tcoffee/seqreformat/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true) ] @@ -39,6 +40,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true) ] diff --git a/modules/nf-core/tcoffee/tcs/tests/main.nf.test b/modules/nf-core/tcoffee/tcs/tests/main.nf.test index d66a2cdaa31..eb7ad821d72 100644 --- a/modules/nf-core/tcoffee/tcs/tests/main.nf.test +++ b/modules/nf-core/tcoffee/tcs/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin.ref", checkIfExists: true) @@ -57,6 +58,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = PIGZ_COMPRESS.out.archive.map { it -> [[ id:'test'], it[1]] } input[1] = [ [ id:'test'], @@ -99,6 +101,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin.ref", checkIfExists: true) @@ -125,6 +128,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin.ref", checkIfExists: true) diff --git a/modules/nf-core/telseq/tests/main.nf.test b/modules/nf-core/telseq/tests/main.nf.test index 02a4e0815b1..569a4d62946 100644 --- a/modules/nf-core/telseq/tests/main.nf.test +++ b/modules/nf-core/telseq/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'cram' ], // meta map file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), @@ -39,6 +40,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'bam' ], // meta map file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), @@ -65,6 +67,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'bambed' ], // meta map file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), @@ -96,6 +99,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'stub', single_end:false ], // meta map file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), diff --git a/modules/nf-core/thermorawfileparser/tests/main.nf.test b/modules/nf-core/thermorawfileparser/tests/main.nf.test index 90f8aa1b046..c21db303f99 100644 --- a/modules/nf-core/thermorawfileparser/tests/main.nf.test +++ b/modules/nf-core/thermorawfileparser/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], // meta map file(params.modules_testdata_base_path + 'proteomics/msspectra/PXD012083_e005640_II.raw', checkIfExists: true) @@ -39,6 +40,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], // meta map file(params.modules_testdata_base_path + 'proteomics/msspectra/PXD012083_e005640_II.raw', checkIfExists: true) diff --git a/modules/nf-core/tiara/tiara/tests/main.nf.test b/modules/nf-core/tiara/tiara/tests/main.nf.test index 8a926a56d17..3b242964dd1 100644 --- a/modules/nf-core/tiara/tiara/tests/main.nf.test +++ b/modules/nf-core/tiara/tiara/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/fasta/test1.contigs.fa.gz', checkIfExists: true) diff --git a/modules/nf-core/tiddit/cov/tests/main.nf.test b/modules/nf-core/tiddit/cov/tests/main.nf.test index 24c273d86dc..04b38b7bcdc 100644 --- a/modules/nf-core/tiddit/cov/tests/main.nf.test +++ b/modules/nf-core/tiddit/cov/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true) @@ -46,6 +47,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) @@ -76,6 +78,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true) @@ -110,6 +113,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) @@ -142,6 +146,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map diff --git a/modules/nf-core/tiddit/sv/tests/main.nf.test b/modules/nf-core/tiddit/sv/tests/main.nf.test index 6e32b9e1cf9..b08aeb5f97e 100644 --- a/modules/nf-core/tiddit/sv/tests/main.nf.test +++ b/modules/nf-core/tiddit/sv/tests/main.nf.test @@ -29,6 +29,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) @@ -61,6 +62,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) @@ -105,6 +107,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true) @@ -136,6 +139,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true) @@ -167,6 +171,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) diff --git a/modules/nf-core/tidk/explore/tests/main.nf.test b/modules/nf-core/tidk/explore/tests/main.nf.test index 4869dab00fa..ac11b71a187 100644 --- a/modules/nf-core/tidk/explore/tests/main.nf.test +++ b/modules/nf-core/tidk/explore/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true) @@ -37,6 +38,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) @@ -61,6 +63,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true) diff --git a/modules/nf-core/tidk/plot/tests/main.nf.test b/modules/nf-core/tidk/plot/tests/main.nf.test index e807d7fc56b..b2ff3779ad7 100644 --- a/modules/nf-core/tidk/plot/tests/main.nf.test +++ b/modules/nf-core/tidk/plot/tests/main.nf.test @@ -31,6 +31,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = TIDK_SEARCH.out.tsv """ } @@ -52,6 +53,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], [] diff --git a/modules/nf-core/tidk/search/tests/main.nf.test b/modules/nf-core/tidk/search/tests/main.nf.test index cb8b5393677..8cd7377d424 100644 --- a/modules/nf-core/tidk/search/tests/main.nf.test +++ b/modules/nf-core/tidk/search/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) @@ -39,6 +40,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) @@ -65,6 +67,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) @@ -90,6 +93,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) diff --git a/modules/nf-core/toulligqc/tests/main.nf.test b/modules/nf-core/toulligqc/tests/main.nf.test index 5bbad941f75..36ffd65a94f 100644 --- a/modules/nf-core/toulligqc/tests/main.nf.test +++ b/modules/nf-core/toulligqc/tests/main.nf.test @@ -12,6 +12,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/nanopore/sequencing_summary/test2.sequencing_summary.txt', checkIfExists: true), @@ -36,6 +37,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/nanopore/sequencing_summary/test2.sequencing_summary.txt', checkIfExists: true), @@ -59,6 +61,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/nanopore/fastq/test.fastq.gz', checkIfExists: true), @@ -82,6 +85,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/nanopore/bam/test.sorted.bam', checkIfExists: true) @@ -107,6 +111,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/nanopore/bam/test.sorted.bam', checkIfExists: true) diff --git a/modules/nf-core/transdecoder/longorf/tests/main.nf.test b/modules/nf-core/transdecoder/longorf/tests/main.nf.test index 30e4305c99d..7216055ac04 100644 --- a/modules/nf-core/transdecoder/longorf/tests/main.nf.test +++ b/modules/nf-core/transdecoder/longorf/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) @@ -45,6 +46,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true) @@ -76,6 +78,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true) diff --git a/modules/nf-core/trimgalore/tests/main.nf.test b/modules/nf-core/trimgalore/tests/main.nf.test index 2a3dbbb0307..d525b4eb1f3 100644 --- a/modules/nf-core/trimgalore/tests/main.nf.test +++ b/modules/nf-core/trimgalore/tests/main.nf.test @@ -12,6 +12,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true) ] ] @@ -51,6 +52,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true) ] ] @@ -71,6 +73,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true), @@ -130,6 +133,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true), diff --git a/modules/nf-core/trimmomatic/tests/main.nf.test b/modules/nf-core/trimmomatic/tests/main.nf.test index e3598c52cbf..e5104db4221 100644 --- a/modules/nf-core/trimmomatic/tests/main.nf.test +++ b/modules/nf-core/trimmomatic/tests/main.nf.test @@ -12,6 +12,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id: 'test', single_end:true ], [ @@ -42,6 +43,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id: 'test', single_end:false ], [ @@ -74,6 +76,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id: 'test', single_end:false ], [ @@ -97,6 +100,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id: 'test', single_end:true ], [ diff --git a/modules/nf-core/trinity/tests/main.nf.test b/modules/nf-core/trinity/tests/main.nf.test index 8717518bd87..b39182402c9 100644 --- a/modules/nf-core/trinity/tests/main.nf.test +++ b/modules/nf-core/trinity/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ @@ -41,6 +42,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map [ @@ -68,6 +70,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ @@ -99,6 +102,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map [ @@ -130,6 +134,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ diff --git a/modules/nf-core/trust4/tests/main.nf.test b/modules/nf-core/trust4/tests/main.nf.test index 7b6c36da0de..21a5758ab64 100644 --- a/modules/nf-core/trust4/tests/main.nf.test +++ b/modules/nf-core/trust4/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:true ], // meta map [], // bam @@ -51,6 +52,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map [], // bam @@ -92,6 +94,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:true ], // meta map [], diff --git a/modules/nf-core/truvari/consistency/tests/main.nf.test b/modules/nf-core/truvari/consistency/tests/main.nf.test index 8d2b2041446..dde0dc2dab9 100644 --- a/modules/nf-core/truvari/consistency/tests/main.nf.test +++ b/modules/nf-core/truvari/consistency/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz', checkIfExists: true), @@ -37,6 +38,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz', checkIfExists: true), @@ -63,6 +65,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz', checkIfExists: true), diff --git a/modules/nf-core/truvari/segment/tests/main.nf.test b/modules/nf-core/truvari/segment/tests/main.nf.test index a51526c8eee..04a5cb28572 100644 --- a/modules/nf-core/truvari/segment/tests/main.nf.test +++ b/modules/nf-core/truvari/segment/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz', checkIfExists: true) @@ -61,6 +62,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz', checkIfExists: true) diff --git a/modules/nf-core/trycycler/cluster/tests/main.nf.test b/modules/nf-core/trycycler/cluster/tests/main.nf.test index e07230afedb..d86aeec58ec 100644 --- a/modules/nf-core/trycycler/cluster/tests/main.nf.test +++ b/modules/nf-core/trycycler/cluster/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface def contigs1 = file("contigs1.fasta") contigs1.text = '>contig_1a\\nATCCCCTTGGACTCCTAGCTAGGCTCTAGAGCCTTCTCTCGACTACGAGCTAGCAGCTACGATCACGACTACAGCACAGCACTACAGCATCAGCACAGCAGTCAGCGA\\n>contig_2a\\nGCTAGGCTCTAACGCGCCATCAGCCGCTCAGCTACGACTATCGCAGCTACGATCAGCATCGATCTAGCAGAGCCTTCTGGTAACGCGACTCAGTCTCTACAGCACGGTAACCAGCACTACAGGGGTTAAGCCCATCA\\n' diff --git a/modules/nf-core/trycycler/subsample/tests/main.nf.test b/modules/nf-core/trycycler/subsample/tests/main.nf.test index 10b20f91b25..628569089de 100644 --- a/modules/nf-core/trycycler/subsample/tests/main.nf.test +++ b/modules/nf-core/trycycler/subsample/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/prokaryotes/candidatus_portiera_aleyrodidarum/nanopore/fastq/test.fastq.gz', checkIfExists: true) diff --git a/modules/nf-core/tsebra/tests/main.nf.test b/modules/nf-core/tsebra/tests/main.nf.test index 6e4511008ca..13cbd1a90e6 100644 --- a/modules/nf-core/tsebra/tests/main.nf.test +++ b/modules/nf-core/tsebra/tests/main.nf.test @@ -42,6 +42,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = GUNZIP_GTF.out.gunzip.map { meta, gtf -> [ meta, [ gtf ] ] } input[1] = GUNZIP_HINTS.out.gunzip.map { meta, gff -> [ gff ] } input[2] = [] @@ -66,6 +67,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ file(params.modules_testdata_base_path + 'genomics/eukaryotes/actinidia_chinensis/genome/chr1/genome.gtf.gz', checkIfExists: true) ] diff --git a/modules/nf-core/tximeta/tximport/tests/main.nf.test b/modules/nf-core/tximeta/tximport/tests/main.nf.test index 5cf6af83edd..69fd9dd90cf 100644 --- a/modules/nf-core/tximeta/tximport/tests/main.nf.test +++ b/modules/nf-core/tximeta/tximport/tests/main.nf.test @@ -46,6 +46,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = UNTAR.out.untar.map { meta, dir -> [ meta, dir.listFiles().collect() ] } input[1] = CUSTOM_TX2GENE.out.tx2gene input[2] = 'kallisto' @@ -77,6 +78,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [], [] ]) input[1] = Channel.of([ [], [] ]) input[2] = 'kallisto' @@ -135,6 +137,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = UNTAR.out.untar.map { meta, dir -> [ meta, dir.listFiles().collect() ] } input[1] = CUSTOM_TX2GENE.out.tx2gene input[2] = 'salmon' @@ -167,6 +170,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [], [] ]) input[1] = Channel.of([ [], [] ]) input[2] = 'salmon' diff --git a/modules/nf-core/ucsc/bedclip/tests/main.nf.test b/modules/nf-core/ucsc/bedclip/tests/main.nf.test index 03458051cf4..70f4f71b692 100644 --- a/modules/nf-core/ucsc/bedclip/tests/main.nf.test +++ b/modules/nf-core/ucsc/bedclip/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bedgraph/test.bedgraph", checkIfExists: true) @@ -38,6 +39,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bedgraph/test.bedgraph", checkIfExists: true) diff --git a/modules/nf-core/ucsc/bedgraphtobigwig/tests/main.nf.test b/modules/nf-core/ucsc/bedgraphtobigwig/tests/main.nf.test index 94a799ef618..83116500d64 100644 --- a/modules/nf-core/ucsc/bedgraphtobigwig/tests/main.nf.test +++ b/modules/nf-core/ucsc/bedgraphtobigwig/tests/main.nf.test @@ -12,6 +12,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test' ], // meta map file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bedgraph/test.bedgraph", checkIfExists: true) @@ -34,6 +35,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test' ], // meta map file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bedgraph/test.bedgraph", checkIfExists: true) diff --git a/modules/nf-core/ucsc/bigwigaverageoverbed/tests/main.nf.test b/modules/nf-core/ucsc/bigwigaverageoverbed/tests/main.nf.test index 927641103d1..13a2391bbe9 100644 --- a/modules/nf-core/ucsc/bigwigaverageoverbed/tests/main.nf.test +++ b/modules/nf-core/ucsc/bigwigaverageoverbed/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id: 'test' ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) ] diff --git a/modules/nf-core/ucsc/gtftogenepred/tests/main.nf.test b/modules/nf-core/ucsc/gtftogenepred/tests/main.nf.test index e0396a63cac..bb17a60fff7 100644 --- a/modules/nf-core/ucsc/gtftogenepred/tests/main.nf.test +++ b/modules/nf-core/ucsc/gtftogenepred/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id: 'test' ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gtf', checkIfExists: true) ] diff --git a/modules/nf-core/ucsc/liftover/tests/main.nf.test b/modules/nf-core/ucsc/liftover/tests/main.nf.test index 8aee1eefc27..80ba46a448d 100644 --- a/modules/nf-core/ucsc/liftover/tests/main.nf.test +++ b/modules/nf-core/ucsc/liftover/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test' ], // meta map file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.bed", checkIfExists: true) @@ -41,6 +42,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test' ], // meta map file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.bed", checkIfExists: true) diff --git a/modules/nf-core/ucsc/wigtobigwig/tests/main.nf.test b/modules/nf-core/ucsc/wigtobigwig/tests/main.nf.test index b48ce0357ba..36dc8ec1f18 100644 --- a/modules/nf-core/ucsc/wigtobigwig/tests/main.nf.test +++ b/modules/nf-core/ucsc/wigtobigwig/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map, file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/wig/test.wig.gz', checkIfExists: true) @@ -38,6 +39,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map, file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/wig/test.wig.gz', checkIfExists: true) diff --git a/modules/nf-core/umitools/dedup/tests/main.nf.test b/modules/nf-core/umitools/dedup/tests/main.nf.test index ab4455366e7..a3136a8e44e 100644 --- a/modules/nf-core/umitools/dedup/tests/main.nf.test +++ b/modules/nf-core/umitools/dedup/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface get_output_stats = false input[0] = [ @@ -44,6 +45,7 @@ nextflow_process { when { process { """ + // testy mctestface get_output_stats = false input[0] = [ @@ -73,6 +75,7 @@ nextflow_process { when { process { """ + // testy mctestface get_output_stats = true input[0] = [ @@ -108,6 +111,7 @@ nextflow_process { when { process { """ + // testy mctestface get_output_stats = false input[0] = [ @@ -137,6 +141,7 @@ nextflow_process { when { process { """ + // testy mctestface get_output_stats = false input[0] = [ @@ -166,6 +171,7 @@ nextflow_process { when { process { """ + // testy mctestface get_output_stats = true input[0] = [ diff --git a/modules/nf-core/umitools/extract/tests/main.nf.test b/modules/nf-core/umitools/extract/tests/main.nf.test index bb8a0658290..89da8b45fcb 100644 --- a/modules/nf-core/umitools/extract/tests/main.nf.test +++ b/modules/nf-core/umitools/extract/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true) ] ] @@ -40,6 +41,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true) ] ] @@ -60,6 +62,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true), file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_2.fastq.gz", checkIfExists: true) ] @@ -88,6 +91,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true), file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_2.fastq.gz", checkIfExists: true) ] diff --git a/modules/nf-core/umitools/prepareforrsem/tests/main.nf.test b/modules/nf-core/umitools/prepareforrsem/tests/main.nf.test index aa31d659396..b345ce0ace2 100644 --- a/modules/nf-core/umitools/prepareforrsem/tests/main.nf.test +++ b/modules/nf-core/umitools/prepareforrsem/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true), @@ -40,6 +41,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true), diff --git a/modules/nf-core/unicycler/tests/main.nf.test b/modules/nf-core/unicycler/tests/main.nf.test index 416b50b8b1f..ab693f31b04 100644 --- a/modules/nf-core/unicycler/tests/main.nf.test +++ b/modules/nf-core/unicycler/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:true ], // meta map [], @@ -40,6 +41,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel.of([ [ id:'test', single_end:true ], // meta map [], diff --git a/modules/nf-core/untar/tests/main.nf.test b/modules/nf-core/untar/tests/main.nf.test index c957517aaa6..ab5e0852084 100644 --- a/modules/nf-core/untar/tests/main.nf.test +++ b/modules/nf-core/untar/tests/main.nf.test @@ -12,6 +12,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/db/kraken2.tar.gz', checkIfExists: true) ] """ } @@ -30,6 +31,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [], file(params.modules_testdata_base_path + 'generic/tar/hello.tar.gz', checkIfExists: true) ] """ } @@ -50,6 +52,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/db/kraken2.tar.gz', checkIfExists: true) ] """ } @@ -70,6 +73,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [], file(params.modules_testdata_base_path + 'generic/tar/hello.tar.gz', checkIfExists: true) ] """ } diff --git a/modules/nf-core/untarfiles/tests/main.nf.test b/modules/nf-core/untarfiles/tests/main.nf.test index 4e3acf5bd72..4b52bb52965 100644 --- a/modules/nf-core/untarfiles/tests/main.nf.test +++ b/modules/nf-core/untarfiles/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id: 'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/db/kraken2.tar.gz', checkIfExists: true) @@ -36,6 +37,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id: 'test'], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bcl/flowcell.tar.gz', checkIfExists: true) @@ -62,6 +64,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id: 'test'], file(params.modules_testdata_base_path + 'generic/tar/hello.tar.gz', checkIfExists: true) @@ -84,6 +87,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id: 'test'], file(params.modules_testdata_base_path + 'generic/tar/hello.tar.gz', checkIfExists: true) diff --git a/modules/nf-core/unzip/tests/main.nf.test b/modules/nf-core/unzip/tests/main.nf.test index df4cb5a6902..22482cd61c0 100644 --- a/modules/nf-core/unzip/tests/main.nf.test +++ b/modules/nf-core/unzip/tests/main.nf.test @@ -37,6 +37,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id: 'hello' ], file(params.modules_testdata_base_path + 'generic/tar/hello.tar.gz', checkIfExists: true) diff --git a/modules/nf-core/unzipfiles/tests/main.nf.test b/modules/nf-core/unzipfiles/tests/main.nf.test index d0164fae336..64bcf6b0a3e 100644 --- a/modules/nf-core/unzipfiles/tests/main.nf.test +++ b/modules/nf-core/unzipfiles/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id: 'hello' ], file(params.modules_testdata_base_path + 'generic/tar/hello.tar.gz', checkIfExists: true) @@ -36,6 +37,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id: 'hello' ], file(params.modules_testdata_base_path + 'generic/tar/hello.tar.gz', checkIfExists: true) diff --git a/modules/nf-core/upd/tests/main.nf.test b/modules/nf-core/upd/tests/main.nf.test index 8e080addf98..d62a2aa3099 100644 --- a/modules/nf-core/upd/tests/main.nf.test +++ b/modules/nf-core/upd/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/ped/justhusky_minimal.vcf.gz', checkIfExists: true) @@ -37,6 +38,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/ped/justhusky_minimal.vcf.gz', checkIfExists: true) diff --git a/modules/nf-core/upp/align/tests/main.nf.test b/modules/nf-core/upp/align/tests/main.nf.test index 7425d984c60..d154e915660 100644 --- a/modules/nf-core/upp/align/tests/main.nf.test +++ b/modules/nf-core/upp/align/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file("https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true) ] @@ -53,6 +54,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test_tree' ], file("https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true) ] @@ -77,6 +79,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], file("https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true) ] diff --git a/modules/nf-core/variantbam/tests/main.nf.test b/modules/nf-core/variantbam/tests/main.nf.test index 11748222d83..65e07f2a598 100644 --- a/modules/nf-core/variantbam/tests/main.nf.test +++ b/modules/nf-core/variantbam/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) @@ -38,6 +39,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) diff --git a/modules/nf-core/varlociraptor/estimatealignmentproperties/tests/main.nf.test b/modules/nf-core/varlociraptor/estimatealignmentproperties/tests/main.nf.test index cc9a493bf02..6f717a85066 100644 --- a/modules/nf-core/varlociraptor/estimatealignmentproperties/tests/main.nf.test +++ b/modules/nf-core/varlociraptor/estimatealignmentproperties/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) @@ -47,6 +48,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) diff --git a/modules/nf-core/vcf2cytosure/tests/main.nf.test b/modules/nf-core/vcf2cytosure/tests/main.nf.test index edd3063d67c..ba03acea394 100644 --- a/modules/nf-core/vcf2cytosure/tests/main.nf.test +++ b/modules/nf-core/vcf2cytosure/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA24385_sv.vcf.gz', checkIfExists: true) ] @@ -45,6 +46,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA24385_sv.vcf.gz', checkIfExists: true) ] diff --git a/modules/nf-core/vcf2db/tests/main.nf.test b/modules/nf-core/vcf2db/tests/main.nf.test index 9532b4325a8..a1c0947d0c3 100644 --- a/modules/nf-core/vcf2db/tests/main.nf.test +++ b/modules/nf-core/vcf2db/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/ped/justhusky_minimal.vcf.gz', checkIfExists: true), @@ -42,6 +43,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/ped/justhusky_minimal.vcf.gz', checkIfExists: true), diff --git a/modules/nf-core/vcf2maf/tests/main.nf.test b/modules/nf-core/vcf2maf/tests/main.nf.test index f17e7740ee6..b7e8f04c24d 100644 --- a/modules/nf-core/vcf2maf/tests/main.nf.test +++ b/modules/nf-core/vcf2maf/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], // meta map file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/gvcf/test.genome.vcf", checkIfExists: true) @@ -55,6 +56,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], // meta map file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/gvcf/test.genome.vcf", checkIfExists: true) diff --git a/modules/nf-core/vcfanno/tests/main.nf.test b/modules/nf-core/vcfanno/tests/main.nf.test index 8bbcfd8942f..bafd49ca680 100644 --- a/modules/nf-core/vcfanno/tests/main.nf.test +++ b/modules/nf-core/vcfanno/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test_compressed', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), @@ -43,6 +44,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test_uncompressed', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true), @@ -75,6 +77,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test_compressed', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), diff --git a/modules/nf-core/vcflib/vcfbreakmulti/tests/main.nf.test b/modules/nf-core/vcflib/vcfbreakmulti/tests/main.nf.test index d9f2113c06b..e7988b38364 100644 --- a/modules/nf-core/vcflib/vcfbreakmulti/tests/main.nf.test +++ b/modules/nf-core/vcflib/vcfbreakmulti/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), @@ -42,6 +43,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), diff --git a/modules/nf-core/vcflib/vcffilter/tests/main.nf.test b/modules/nf-core/vcflib/vcffilter/tests/main.nf.test index 57054988608..0a07d85028f 100644 --- a/modules/nf-core/vcflib/vcffilter/tests/main.nf.test +++ b/modules/nf-core/vcflib/vcffilter/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), diff --git a/modules/nf-core/vcflib/vcffixup/tests/main.nf.test b/modules/nf-core/vcflib/vcffixup/tests/main.nf.test index b17eaae79d9..cc69609ef07 100644 --- a/modules/nf-core/vcflib/vcffixup/tests/main.nf.test +++ b/modules/nf-core/vcflib/vcffixup/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true) @@ -38,6 +39,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true) diff --git a/modules/nf-core/vcflib/vcfuniq/tests/main.nf.test b/modules/nf-core/vcflib/vcfuniq/tests/main.nf.test index 71c12072abd..b19c1bbc37b 100644 --- a/modules/nf-core/vcflib/vcfuniq/tests/main.nf.test +++ b/modules/nf-core/vcflib/vcfuniq/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), diff --git a/modules/nf-core/vcftools/tests/main.nf.test b/modules/nf-core/vcftools/tests/main.nf.test index d8f578dac18..4fdbe596ba2 100644 --- a/modules/nf-core/vcftools/tests/main.nf.test +++ b/modules/nf-core/vcftools/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) @@ -43,6 +44,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true) @@ -71,6 +73,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) @@ -99,6 +102,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true) @@ -127,6 +131,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true) diff --git a/modules/nf-core/velocyto/tests/main.nf.test b/modules/nf-core/velocyto/tests/main.nf.test index 0679e37c21b..b39d8692942 100644 --- a/modules/nf-core/velocyto/tests/main.nf.test +++ b/modules/nf-core/velocyto/tests/main.nf.test @@ -32,6 +32,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = Channel .fromList( [ @@ -74,6 +75,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'Sample_X' ], // meta map file(params.modules_testdata_base_path + 'genomics/mus_musculus/rna_velocity/barcodes.tsv.gz', checkIfExists: true), @@ -114,6 +116,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'Sample_X' ], // meta map file(params.modules_testdata_base_path + 'genomics/mus_musculus/rna_velocity/barcodes.tsv.gz', checkIfExists: true), diff --git a/modules/nf-core/verifybamid/verifybamid/tests/main.nf.test b/modules/nf-core/verifybamid/verifybamid/tests/main.nf.test index c938ce02d67..cd2a0d420d4 100644 --- a/modules/nf-core/verifybamid/verifybamid/tests/main.nf.test +++ b/modules/nf-core/verifybamid/verifybamid/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) diff --git a/modules/nf-core/vg/construct/tests/main.nf.test b/modules/nf-core/vg/construct/tests/main.nf.test index aa58aefab58..4976192c27a 100644 --- a/modules/nf-core/vg/construct/tests/main.nf.test +++ b/modules/nf-core/vg/construct/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz', checkIfExists: true), @@ -47,6 +48,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], // meta map file(params.modules_testdata_base_path + 'pangenomics/homo_sapiens/pangenome.fa', checkIfExists: true), @@ -73,6 +75,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz', checkIfExists: true), @@ -105,6 +108,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz', checkIfExists: true), diff --git a/modules/nf-core/vg/deconstruct/tests/main.nf.test b/modules/nf-core/vg/deconstruct/tests/main.nf.test index 6b73a48fc97..ce6f298e620 100644 --- a/modules/nf-core/vg/deconstruct/tests/main.nf.test +++ b/modules/nf-core/vg/deconstruct/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map [ file(params.modules_testdata_base_path + 'pangenomics/homo_sapiens/pangenome.gfaffix.gfa', checkIfExists: true) ] diff --git a/modules/nf-core/vg/index/tests/main.nf.test b/modules/nf-core/vg/index/tests/main.nf.test index fdec7348fcc..f3594c66892 100644 --- a/modules/nf-core/vg/index/tests/main.nf.test +++ b/modules/nf-core/vg/index/tests/main.nf.test @@ -41,6 +41,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = VG_CONSTRUCT.out.graph """ @@ -60,6 +61,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = VG_CONSTRUCT.out.graph """ diff --git a/modules/nf-core/viennarna/rnacofold/tests/main.nf.test b/modules/nf-core/viennarna/rnacofold/tests/main.nf.test index 305018b0ba3..c5ecfebdf2d 100644 --- a/modules/nf-core/viennarna/rnacofold/tests/main.nf.test +++ b/modules/nf-core/viennarna/rnacofold/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id: 'test'], file(params.modules_testdata_base_path + 'delete_me/viennarna/rnacofold/test.fa', checkIfExists: true) @@ -38,6 +39,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id: 'test'], file(params.modules_testdata_base_path + 'delete_me/viennarna/rnacofold/test.fa', checkIfExists: true) diff --git a/modules/nf-core/viennarna/rnafold/tests/main.nf.test b/modules/nf-core/viennarna/rnafold/tests/main.nf.test index 6a41dba15ae..0e4a7554faf 100644 --- a/modules/nf-core/viennarna/rnafold/tests/main.nf.test +++ b/modules/nf-core/viennarna/rnafold/tests/main.nf.test @@ -13,7 +13,8 @@ nextflow_process { when { process { - """ + """ + // testy mctestface input[0] = [ [:], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/transcriptome.fasta", checkIfExists: true) @@ -36,7 +37,8 @@ nextflow_process { when { process { - """ + """ + // testy mctestface input[0] = [ [:], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/transcriptome.fasta", checkIfExists: true) diff --git a/modules/nf-core/viennarna/rnalfold/tests/main.nf.test b/modules/nf-core/viennarna/rnalfold/tests/main.nf.test index 803e9cb7f89..bebfceb5414 100644 --- a/modules/nf-core/viennarna/rnalfold/tests/main.nf.test +++ b/modules/nf-core/viennarna/rnalfold/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/transcriptome.fasta', checkIfExists: true) """ } @@ -34,6 +35,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/transcriptome.fasta', checkIfExists: true) """ } diff --git a/modules/nf-core/vireo/tests/main.nf.test b/modules/nf-core/vireo/tests/main.nf.test index 86ba742b2ee..50f97ce09bd 100644 --- a/modules/nf-core/vireo/tests/main.nf.test +++ b/modules/nf-core/vireo/tests/main.nf.test @@ -42,6 +42,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = CELLSNP_MODEA.out.cell.collect{ meta, cell -> cell }.map{ cell -> [[id:'test'], cell, @@ -68,6 +69,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [[id:'sample1'], [], 2, diff --git a/modules/nf-core/vrhyme/vrhyme/tests/main.nf.test b/modules/nf-core/vrhyme/vrhyme/tests/main.nf.test index 5ff7f4e2dc9..03e9707225a 100644 --- a/modules/nf-core/vrhyme/vrhyme/tests/main.nf.test +++ b/modules/nf-core/vrhyme/vrhyme/tests/main.nf.test @@ -32,6 +32,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ @@ -64,6 +65,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ diff --git a/modules/nf-core/vsearch/cluster/tests/main.nf.test b/modules/nf-core/vsearch/cluster/tests/main.nf.test index 155a949d162..c3fea20defd 100644 --- a/modules/nf-core/vsearch/cluster/tests/main.nf.test +++ b/modules/nf-core/vsearch/cluster/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) @@ -40,6 +41,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) @@ -64,6 +66,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) @@ -88,6 +91,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) @@ -112,6 +116,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) diff --git a/modules/nf-core/vsearch/dereplicate/tests/main.nf.test b/modules/nf-core/vsearch/dereplicate/tests/main.nf.test index 470b1b60172..041be15dc36 100644 --- a/modules/nf-core/vsearch/dereplicate/tests/main.nf.test +++ b/modules/nf-core/vsearch/dereplicate/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ "id": "ERR2537816", "single_end": false ], file("https://raw.githubusercontent.com/nf-core/test-datasets/phyloplace/testdata/cyn_syn.fna", checkIfExists: true) @@ -38,6 +39,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ "id": "ERR2537816", "single_end": false ], file("https://raw.githubusercontent.com/nf-core/test-datasets/phyloplace/testdata/cyn_syn.fna", checkIfExists: true) diff --git a/modules/nf-core/vsearch/fastqfilter/tests/main.nf.test b/modules/nf-core/vsearch/fastqfilter/tests/main.nf.test index dfc881aec37..dc28a0ce195 100644 --- a/modules/nf-core/vsearch/fastqfilter/tests/main.nf.test +++ b/modules/nf-core/vsearch/fastqfilter/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id:'test'], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), @@ -44,6 +45,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id:'test'], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), diff --git a/modules/nf-core/vsearch/sintax/tests/main.nf.test b/modules/nf-core/vsearch/sintax/tests/main.nf.test index ebad65cbba7..00ef8a6b1eb 100644 --- a/modules/nf-core/vsearch/sintax/tests/main.nf.test +++ b/modules/nf-core/vsearch/sintax/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [[id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)] input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/transcriptome.fasta', checkIfExists: true) diff --git a/modules/nf-core/vsearch/sort/tests/main.nf.test b/modules/nf-core/vsearch/sort/tests/main.nf.test index 3ea3ade7cf6..1395cd46cb6 100644 --- a/modules/nf-core/vsearch/sort/tests/main.nf.test +++ b/modules/nf-core/vsearch/sort/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) @@ -39,6 +40,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) diff --git a/modules/nf-core/vsearch/usearchglobal/tests/main.nf.test b/modules/nf-core/vsearch/usearchglobal/tests/main.nf.test index 756895b41a0..ff0d756d1fa 100644 --- a/modules/nf-core/vsearch/usearchglobal/tests/main.nf.test +++ b/modules/nf-core/vsearch/usearchglobal/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [[id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/transcriptome.fasta', checkIfExists: true)] input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) input[2] = 0.985 @@ -43,6 +44,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [[id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/transcriptome.fasta', checkIfExists: true)] input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) input[2] = 0.985 diff --git a/modules/nf-core/vt/decompose/tests/main.nf.test b/modules/nf-core/vt/decompose/tests/main.nf.test index a23a34cc8ce..b60c0eeb68a 100644 --- a/modules/nf-core/vt/decompose/tests/main.nf.test +++ b/modules/nf-core/vt/decompose/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), @@ -39,6 +40,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true), diff --git a/modules/nf-core/vt/normalize/tests/main.nf.test b/modules/nf-core/vt/normalize/tests/main.nf.test index ae7505679f0..a6b769ae6e1 100644 --- a/modules/nf-core/vt/normalize/tests/main.nf.test +++ b/modules/nf-core/vt/normalize/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz', checkIfExists: true), @@ -53,6 +54,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz', checkIfExists: true), @@ -90,6 +92,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz', checkIfExists: true), @@ -124,6 +127,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz', checkIfExists: true), diff --git a/modules/nf-core/wfmash/tests/main.nf.test b/modules/nf-core/wfmash/tests/main.nf.test index 721541dd558..b7297dc7da6 100644 --- a/modules/nf-core/wfmash/tests/main.nf.test +++ b/modules/nf-core/wfmash/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'pangenomics/homo_sapiens/pangenome.fa.gz', checkIfExists: true), diff --git a/modules/nf-core/wgsim/tests/main.nf.test b/modules/nf-core/wgsim/tests/main.nf.test index 41b8d64acc8..71f755e99cc 100644 --- a/modules/nf-core/wgsim/tests/main.nf.test +++ b/modules/nf-core/wgsim/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] @@ -41,6 +42,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] @@ -68,6 +70,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] diff --git a/modules/nf-core/whamg/tests/main.nf.test b/modules/nf-core/whamg/tests/main.nf.test index 9dc5e77f4e5..302ae23c1b5 100644 --- a/modules/nf-core/whamg/tests/main.nf.test +++ b/modules/nf-core/whamg/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), diff --git a/modules/nf-core/windowmasker/convert/tests/main.nf.test b/modules/nf-core/windowmasker/convert/tests/main.nf.test index 8118cdf3100..0088dc756a1 100644 --- a/modules/nf-core/windowmasker/convert/tests/main.nf.test +++ b/modules/nf-core/windowmasker/convert/tests/main.nf.test @@ -29,6 +29,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = WINDOWMASKER_MKCOUNTS.out.counts """ } @@ -48,6 +49,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = WINDOWMASKER_MKCOUNTS.out.counts """ } @@ -67,6 +69,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = WINDOWMASKER_MKCOUNTS.out.counts """ } @@ -88,6 +91,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id: "test" ], [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)] diff --git a/modules/nf-core/windowmasker/mkcounts/tests/main.nf.test b/modules/nf-core/windowmasker/mkcounts/tests/main.nf.test index bf53d7fa642..fc4e6464d78 100644 --- a/modules/nf-core/windowmasker/mkcounts/tests/main.nf.test +++ b/modules/nf-core/windowmasker/mkcounts/tests/main.nf.test @@ -41,6 +41,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id: "test" ], [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)] diff --git a/modules/nf-core/windowmasker/ustat/tests/main.nf.test b/modules/nf-core/windowmasker/ustat/tests/main.nf.test index 6e02c9c18c4..ef9084f1553 100644 --- a/modules/nf-core/windowmasker/ustat/tests/main.nf.test +++ b/modules/nf-core/windowmasker/ustat/tests/main.nf.test @@ -30,6 +30,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = WINDOWMASKER_MKCOUNTS.out.counts input[1] = [ [id: "test" ], @@ -48,6 +49,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = WINDOWMASKER_MKCOUNTS.out.counts input[1] = [ [id: "test" ], diff --git a/modules/nf-core/wisecondorx/convert/tests/main.nf.test b/modules/nf-core/wisecondorx/convert/tests/main.nf.test index d0095513f2e..e4c17135280 100644 --- a/modules/nf-core/wisecondorx/convert/tests/main.nf.test +++ b/modules/nf-core/wisecondorx/convert/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.sorted.bam', checkIfExists: true), @@ -43,6 +44,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), @@ -82,6 +84,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.sorted.bam', checkIfExists: true), diff --git a/modules/nf-core/wisecondorx/gender/tests/main.nf.test b/modules/nf-core/wisecondorx/gender/tests/main.nf.test index c513f611764..c6c023d2ff1 100644 --- a/modules/nf-core/wisecondorx/gender/tests/main.nf.test +++ b/modules/nf-core/wisecondorx/gender/tests/main.nf.test @@ -35,6 +35,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = WISECONDORX_CONVERT.out.npz input[1] = [ [ id: "reference" ], diff --git a/modules/nf-core/wisecondorx/newref/tests/main.nf.test b/modules/nf-core/wisecondorx/newref/tests/main.nf.test index 3645d7734ef..b49eddad48c 100644 --- a/modules/nf-core/wisecondorx/newref/tests/main.nf.test +++ b/modules/nf-core/wisecondorx/newref/tests/main.nf.test @@ -40,6 +40,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = WISECONDORX_CONVERT.out.npz .map { meta, npz -> new_meta = meta + [id:"combined"] diff --git a/modules/nf-core/wisecondorx/predict/tests/main.nf.test b/modules/nf-core/wisecondorx/predict/tests/main.nf.test index 2c8ee4d7149..e28fe66e1d9 100644 --- a/modules/nf-core/wisecondorx/predict/tests/main.nf.test +++ b/modules/nf-core/wisecondorx/predict/tests/main.nf.test @@ -35,6 +35,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = WISECONDORX_CONVERT.out.npz input[1] = [ [ id:'reference' ], diff --git a/modules/nf-core/wittyer/tests/main.nf.test b/modules/nf-core/wittyer/tests/main.nf.test index c7e0778d0ed..ff8839bbabe 100644 --- a/modules/nf-core/wittyer/tests/main.nf.test +++ b/modules/nf-core/wittyer/tests/main.nf.test @@ -44,6 +44,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = TABIX_BGZIP_1.out.output.join(TABIX_BGZIP_2.out.output).map{meta, vcf1, vcf2 -> tuple(meta, vcf1, vcf2, [], [])} """ } @@ -68,6 +69,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = TABIX_BGZIP_1.out.output .join(TABIX_BGZIP_2.out.output) .map{meta, vcf1, vcf2 -> @@ -98,6 +100,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = TABIX_BGZIP_1.out.output .join(TABIX_BGZIP_2.out.output) .map{meta, vcf1, vcf2 -> @@ -130,6 +133,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test_stub', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/chr21/simulated_sv.vcf.gz', checkIfExists: true), diff --git a/modules/nf-core/xengsort/index/tests/main.nf.test b/modules/nf-core/xengsort/index/tests/main.nf.test index 069a432e603..f5b656ad21a 100644 --- a/modules/nf-core/xengsort/index/tests/main.nf.test +++ b/modules/nf-core/xengsort/index/tests/main.nf.test @@ -16,6 +16,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) input[2] = 'index' diff --git a/modules/nf-core/xz/compress/tests/main.nf.test b/modules/nf-core/xz/compress/tests/main.nf.test index 7087d15e468..b446456c8b0 100644 --- a/modules/nf-core/xz/compress/tests/main.nf.test +++ b/modules/nf-core/xz/compress/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) @@ -33,6 +34,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) diff --git a/modules/nf-core/xz/decompress/tests/main.nf.test b/modules/nf-core/xz/decompress/tests/main.nf.test index 281e7106038..5d6d8c77331 100644 --- a/modules/nf-core/xz/decompress/tests/main.nf.test +++ b/modules/nf-core/xz/decompress/tests/main.nf.test @@ -27,6 +27,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = XZ_COMPRESS.out.archive """ } @@ -44,6 +45,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test'], // meta map file("test.xz") diff --git a/modules/nf-core/yahs/tests/main.nf.test b/modules/nf-core/yahs/tests/main.nf.test index ee53a110d92..d20e6b44e84 100644 --- a/modules/nf-core/yahs/tests/main.nf.test +++ b/modules/nf-core/yahs/tests/main.nf.test @@ -36,6 +36,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = SAMTOOLS_VIEW.out.bam input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) diff --git a/modules/nf-core/yak/count/tests/main.nf.test b/modules/nf-core/yak/count/tests/main.nf.test index 8a003d71f2f..8ae95567c37 100644 --- a/modules/nf-core/yak/count/tests/main.nf.test +++ b/modules/nf-core/yak/count/tests/main.nf.test @@ -13,7 +13,8 @@ nextflow_process { when { process { - """ + """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true) @@ -35,7 +36,8 @@ nextflow_process { when { process { - """ + """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true), diff --git a/modules/nf-core/yara/index/tests/main.nf.test b/modules/nf-core/yara/index/tests/main.nf.test index 5d98331107b..feb393b609a 100644 --- a/modules/nf-core/yara/index/tests/main.nf.test +++ b/modules/nf-core/yara/index/tests/main.nf.test @@ -14,6 +14,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) @@ -38,6 +39,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) diff --git a/modules/nf-core/yara/mapper/tests/main.nf.test b/modules/nf-core/yara/mapper/tests/main.nf.test index 4fe95f35c13..7bb6bfa2d38 100644 --- a/modules/nf-core/yara/mapper/tests/main.nf.test +++ b/modules/nf-core/yara/mapper/tests/main.nf.test @@ -27,6 +27,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) @@ -57,6 +58,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:true ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) @@ -80,6 +82,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), @@ -115,6 +118,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), diff --git a/modules/nf-core/zip/tests/main.nf.test b/modules/nf-core/zip/tests/main.nf.test index 9652841d360..d3cb5837c4a 100644 --- a/modules/nf-core/zip/tests/main.nf.test +++ b/modules/nf-core/zip/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_process { when { process { """ + // testy mctestface input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ]