port parabricks/mutectcaller to nf-test #19433
Workflow file for this run
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| name: Run pytest-workflow | |
| 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 }} | |
| # renovate: datasource=github-releases depName=nextflow-io/nextflow versioning=semver | |
| NXF_VER: "24.10.1" | |
| jobs: | |
| pytest-changes: | |
| name: pytest-changes | |
| runs-on: ubuntu-latest | |
| outputs: | |
| tags: ${{ steps.filter.outputs.changes }} | |
| modules: ${{ steps.tags.outputs.modules }} | |
| subworkflows: ${{ steps.tags.outputs.subworkflows }} | |
| steps: | |
| - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 | |
| with: | |
| fetch-depth: 2 # To retrieve the preceding commit. | |
| - uses: dorny/paths-filter@de90cc6fb38fc0963ad72b210f1f284cd68cea36 # v3 | |
| id: filter | |
| with: | |
| filters: "tests/config/pytest_modules.yml" | |
| token: "" | |
| - name: Fetch module tags | |
| id: tags | |
| run: | | |
| echo modules=$(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 }} | |
| 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@1bd1e32a3bdc45362d1e726936510720a7c30a57 # 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 | |
| uses: nf-core/setup-nextflow@v2 | |
| with: | |
| version: ${{ env.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: "3.11" | |
| - 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 | |
| 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) }}" |