.github/workflows/test.yml

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/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@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: modules/nf-core/parabricks/fq2bammeth
          - profile: docker_self_hosted
            path: modules/nf-core/parabricks/fq2bammeth
          - profile: singularity
            path: modules/nf-core/parabricks/fq2bammeth
          - profile: conda
            path: modules/nf-core/parabricks/fq2bam
          - profile: docker_self_hosted
            path: modules/nf-core/parabricks/fq2bam
          - profile: singularity
            path: modules/nf-core/parabricks/fq2bam
          - 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
          - profile: conda
            path: modules/nf-core/xeniumranger/relabel
          - profile: conda
            path: modules/nf-core/xeniumranger/rename
          - profile: conda
            path: modules/nf-core/xeniumranger/resegment
          - profile: conda
            path: modules/nf-core/xeniumranger/import-segmentation

    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) }}"