Update CI and fix Singularity Bug #11
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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, develop] | |
| merge_group: | |
| types: [checks_requested] | |
| branches: [master, develop] | |
| workflow_dispatch: {} | |
| # 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: "24.10.2" | |
| 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 ${{ steps.tags.outputs.subworkflows }} | |
| pytest: | |
| runs-on: ubuntu-latest | |
| name: pytest | |
| needs: [pytest-changes] | |
| if: needs.pytest-changes.outputs.tags != '[]' | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| tags: ["${{ fromJson(needs.pytest-changes.outputs.tags) }}"] | |
| profile: [conda, docker, singularity] | |
| exclude: | |
| - tags: "nf-test" | |
| - profile: "conda" | |
| tags: gbcms | |
| - profile: "conda" | |
| tags: polysolver | |
| - profile: "conda" | |
| tags: snppileup | |
| - profile: "conda" | |
| tags: facets | |
| - profile: "conda" | |
| tags: mutect1 | |
| - profile: "conda" | |
| tags: phylowgs/createinput | |
| - profile: "conda" | |
| tags: phylowgs/parsecnvs | |
| - profile: "conda" | |
| tags: phylowgs/multievolve | |
| - profile: "conda" | |
| tags: phylowgs/writeresults | |
| - profile: "conda" | |
| tags: netmhcpan4 | |
| - profile: "conda" | |
| tags: neoantigeninput | |
| - profile: "conda" | |
| tags: neoantigenediting/aligntoIEDB | |
| - profile: "conda" | |
| tags: neoantigenediting/computeFitness | |
| - profile: "conda" | |
| tags: subworkflows/neoantigen_editing | |
| - profile: "conda" | |
| tags: subworkflows/phylowgs | |
| - profile: "conda" | |
| tags: netmhcstabpan | |
| - profile: "conda" | |
| tags: ppflagfixer | |
| - profile: "conda" | |
| tags: neoantigenutils/generatemutfasta | |
| - profile: "conda" | |
| tags: neoantigenutils/formatnetmhcpan | |
| - profile: "conda" | |
| tags: neoantigenutils/generatehlastring | |
| - profile: "conda" | |
| tags: neoantigenutils/neoantigeninput | |
| - profile: "conda" | |
| tags: subworkflows/netmhcstabandpan | |
| - profile: "conda" | |
| tags: salmon/index | |
| - profile: "conda" | |
| tags: genomenexus/vcf2maf | |
| - profile: "conda" | |
| tags: genomenexus/annotationpipeline | |
| - profile: "conda" | |
| tags: ppflagfixer | |
| - profile: "conda" | |
| tags: pvmaf/tagtraceback | |
| - profile: "conda" | |
| tags: pvmaf/concat | |
| - profile: "conda" | |
| tags: genotypevariants/all | |
| - profile: "conda" | |
| tags: subworkflows/traceback | |
| - profile: "conda" | |
| tags: salmon/index | |
| - profile: "conda" | |
| tags: subworkflows/genome_nexus | |
| - profile: "conda" | |
| tags: salmon/quant | |
| - profile: "conda" | |
| tags: rediscoverte | |
| - profile: "conda" | |
| tags: neosv | |
| - profile: "conda" | |
| tags: netmhc3 | |
| 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 $NXF_SINGULARITY_LIBRARYDIR | |
| - name: Conda setup | |
| if: matrix.profile == 'conda' | |
| uses: conda-incubator/setup-miniconda@d2e6a045a86077fb6cad6f5adf368e9076ddaa8d # v3 | |
| with: | |
| auto-update-conda: true | |
| conda-solver: libmamba | |
| conda-remove-defaults: true | |
| # Test the module | |
| - name: Run pytest-workflow | |
| # only use one thread for pytest-workflow to avoid race condition on conda cache. | |
| run: TMPDIR=~ PROFILE=${{ 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) }}" |