Fastq align dedup bwameth #17351
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| name: Run tests | ||
| on: | ||
| push: | ||
| branches: | ||
| # https://docs.renovatebot.com/key-concepts/automerge/#branch-vs-pr-automerging | ||
| - "renovate/**" # branches Renovate creates | ||
| 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 | ||
| with: | ||
| python-version: "3.11" | ||
| - 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: ${{ steps.tags.outputs.subworkflows }} | ||
| steps: | ||
| - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 | ||
| with: | ||
| fetch-depth: 2 # To retrieve the preceding commit. | ||
| - uses: dorny/paths-filter@de90cc6fb38fc0963ad72b210f1f284cd68cea36 # v3 | ||
| id: filter | ||
| with: | ||
| filters: "tests/config/pytest_modules.yml" | ||
| token: "" | ||
| - name: Fetch module tags | ||
| id: tags | ||
| run: | | ||
| echo modules=$(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.filter.outputs.components }} | ||
| echo ${{ steps.outputs.outputs.modules }} | ||
| echo ${{ steps.outputs.outputs.subworkflows }} | ||
| nf-core-lint-modules: | ||
| runs-on: ${{ github.event.inputs.runners || 'ubuntu-latest' }} | ||
| 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: ${{ github.event.inputs.runners || 'ubuntu-latest' }} | ||
| name: pytest | ||
| needs: [pytest-changes] | ||
| if: needs.pytest-changes.outputs.tags != '[]' | ||
| strategy: | ||
| fail-fast: false | ||
| matrix: | ||
| tags: ["${{ 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/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@d2e6a045a86077fb6cad6f5adf368e9076ddaa8d # v3 | ||
| with: | ||
| miniconda-version: "latest" | ||
| channels: conda-forge,bioconda | ||
| python-version: ${{ matrix.python-version }} | ||
| conda-remove-defaults: true | ||
| - 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/deepsomatic | ||
| - profile: singularity | ||
| path: modules/nf-core/deepsomatic | ||
| - 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/doubletdetection | ||
| - 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 | ||
| - 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 | ||
| steps: | ||
| - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 | ||
| - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5 | ||
| - name: Run nf-test Action | ||
| uses: ./.github/actions/nf-test-action | ||
| with: | ||
| path: ${{ matrix.path }} | ||
| profile: ${{ matrix.profile }} | ||
| nf-test-gpu: | ||
| runs-on: "gpu" | ||
| name: nf-test-gpu | ||
| needs: [nf-test-changes] | ||
| if: ( needs.nf-test-changes.outputs.paths != '[]' && contains(needs.nf-test-changes.outputs.paths, 'modules/nf-core/parabricks', 'subworkflows/nf-core/fastq_align_dedup_bwameth') ) | ||
|
Check failure on line 690 in .github/workflows/test.yml
|
||
| strategy: | ||
| fail-fast: false | ||
| matrix: | ||
| include: | ||
| - path: modules/nf-core/parabricks/applybqsr | ||
| profile: [docker_self_hosted, singularity] | ||
| - path: modules/nf-core/parabricks/fq2bam | ||
| profile: [docker_self_hosted, singularity] | ||
| - path: modules/nf-core/parabricks/fq2bammeth | ||
| profile: [docker_self_hosted, singularity] | ||
| - path: subworkflows/nf-core/fastq_align_dedup_bwameth | ||
| profile: [docker_self_hosted, singularity] | ||
| env: | ||
| NXF_ANSI_LOG: false | ||
| steps: | ||
| - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 | ||
| - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5 | ||
| - name: Run nf-test Action | ||
| uses: ./.github/actions/nf-test-action | ||
| env: | ||
| SENTIEON_ENCRYPTION_KEY: ${{ secrets.SENTIEON_ENCRYPTION_KEY }} | ||
| SENTIEON_LICENSE_MESSAGE: ${{ secrets.SENTIEON_LICENSE_MESSAGE }} | ||
| SENTIEON_LICSRVR_IP: ${{ secrets.SENTIEON_LICSRVR_IP }} | ||
| SENTIEON_AUTH_MECH: "GitHub Actions - token" | ||
| with: | ||
| path: ${{ matrix.path }} | ||
| profile: ${{ matrix.profile }},gpu | ||
| 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, | ||
| nf-test-gpu, | ||
| ] | ||
| 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) }}" | ||
