parabricks/applybqsr version updated and tests migrated to nf-test #16646
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| 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@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 | |
| - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # 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@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 | |
| - name: Install NodeJS | |
| uses: actions/setup-node@39370e3970a6d050c480ffad4ff0ed4d3fdee5af # 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@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 | |
| - uses: actions/setup-node@39370e3970a6d050c480ffad4ff0ed4d3fdee5af # 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: ${{ steps.tags.outputs.subworkflows }} | |
| steps: | |
| - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 | |
| with: | |
| fetch-depth: 2 # To retrieve the preceding commit. | |
| # TODO: change back to using dorny/paths-filter when https://github.com/dorny/paths-filter/pull/133 is implemented | |
| - uses: mirpedrol/paths-filter@main | |
| id: filter | |
| with: | |
| filters: "tests/config/pytest_modules.yml" | |
| token: "" | |
| - name: Fetch module tags | |
| id: tags | |
| run: | | |
| echo modules=$(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@11bd71901bbe5b1630ceea73d27597364c9af683 # 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@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5 | |
| with: | |
| python-version: "3.11" | |
| - uses: actions/cache@6849a6489940f00c2f30c0fb92c6274307ccb58a # 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@8df1039502a15bceb9433410b1a100fbe190c53b # 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@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5 | |
| with: | |
| python-version: "3.11" | |
| - name: Install pip | |
| run: python -m pip install --upgrade pip | |
| - uses: actions/setup-java@8df1039502a15bceb9433410b1a100fbe190c53b # 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/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@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5 | |
| with: | |
| python-version: "3.11" | |
| - uses: actions/cache@6849a6489940f00c2f30c0fb92c6274307ccb58a # 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@8df1039502a15bceb9433410b1a100fbe190c53b # 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@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # 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/deepvariant/vcfstatsreport | |
| - 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 | |
| - profile: conda | |
| path: subworkflows/nf-core/fasta_newick_epang_gappa | |
| - path: modules/nf-core/parabricks/fq2bammeth | |
| - path: modules/nf-core/parabricks/fq2bam | |
| - path: modules/nf-core/parabricks/applybqsr | |
| 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@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 | |
| - uses: actions/setup-java@8df1039502a15bceb9433410b1a100fbe190c53b # 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@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5 | |
| with: | |
| python-version: "3.11" | |
| - uses: actions/cache@6849a6489940f00c2f30c0fb92c6274307ccb58a # 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 | |
| if: ${{ matrix.path != '' }} | |
| 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 | |
| if: ${{ matrix.path != '' }} | |
| with: | |
| path: >- | |
| test.tap | |
| - name: Clean up | |
| if: always() | |
| run: | | |
| sudo rm -rf /home/ubuntu/tests/ | |
| nf-test-gpu: | |
| runs-on: ${{ github.event.inputs.runners || 'gpu' }} | |
| name: nf-test | |
| needs: [nf-test-changes] | |
| if: ( needs.nf-test-changes.outputs.paths != '[]' ) | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| path: ["${{ fromJson(needs.nf-test-changes.outputs.paths) }}"] | |
| profile: [conda, docker_self_hosted, singularity] | |
| include: | |
| - path: modules/nf-core/parabricks/applybqsr | |
| - path: modules/nf-core/parabricks/fq2bam | |
| - path: modules/nf-core/parabricks/fq2bammeth | |
| exclude: | |
| - profile: conda | |
| path: modules/nf-core/parabricks/fq2bam | |
| - profile: conda | |
| path: modules/nf-core/parabricks/fq2bammeth | |
| - profile: conda | |
| path: modules/nf-core/parabricks/applybqsr | |
| 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@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 | |
| - uses: actions/setup-java@8df1039502a15bceb9433410b1a100fbe190c53b # 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@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5 | |
| with: | |
| python-version: "3.11" | |
| - uses: actions/cache@6849a6489940f00c2f30c0fb92c6274307ccb58a # 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 | |
| if: ${{ matrix.path != '' }} | |
| 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 | |
| if: ${{ matrix.path != '' }} | |
| 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) }}" |