Update docs for ancestry release #687
Workflow file for this run
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| name: CI | |
| on: | |
| push: | |
| branches: | |
| - dev | |
| - main | |
| - ci | |
| pull_request: | |
| branches: | |
| - dev | |
| - main | |
| release: | |
| types: [published] | |
| env: | |
| SINGULARITY_VERSION: "3.8.3" | |
| NXF_ANSI_LOG: false | |
| CAPSULE_LOG: none | |
| NXF_SINGULARITY_CACHEDIR: "${{ github.workspace }}/singularity" | |
| jobs: | |
| preload_docker: | |
| name: Preload docker images | |
| if: ${{ github.event_name == 'push'}} | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@v3 | |
| - name: Cache docker | |
| id: cache-docker | |
| uses: actions/cache@v3 | |
| with: | |
| path: ${{ runner.temp }}/docker | |
| key: ${{ runner.os }}-${{ github.sha }} | |
| - name: Pull and save docker | |
| if: matrix.profile == 'docker' && ${{ steps.cache-docker.outputs.cache-hit != 'true' }} | |
| run: | | |
| git grep 'ext.docker*' ${{ github.workspace }}/conf/modules.config | cut -f 2 -d '=' | xargs -L 2 echo | tr -d ' ' > ${{ runner.temp }}/images.txt | |
| cat ${{ runner.temp }}/images.txt | xargs -I {} sh -c 'docker pull --platform linux/amd64 "$1"' - {} | |
| mkdir -p ${{ runner.temp }}/docker/ | |
| cat ${{ runner.temp }}/images.txt | xargs -I {} sh -c 'docker save "$1" > ${{ runner.temp }}/docker/$(basename "$1").tar' - {} | |
| preload_singularity: | |
| name: Preload singularity images | |
| if: ${{ github.event_name == 'push'}} | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@v3 | |
| - name: Cache singularity setup | |
| id: cache-singularity-setup | |
| uses: actions/cache@v3 | |
| with: | |
| path: /opt/hostedtoolcache/singularity/${{ env.SINGULARITY_VERSION }}/x64 | |
| key: ${{ runner.os }}-singularity-${{ env.SINGULARITY_VERSION }} | |
| - name: Set up Singularity | |
| uses: eWaterCycle/setup-singularity@v7 | |
| if: ${{ steps.cache-singularity-setup.outputs.cache-hit != 'true' }} | |
| with: | |
| singularity-version: ${{ env.SINGULARITY_VERSION }} | |
| - name: Add singularity to path | |
| if: steps.cache-singularity-setup.outputs.cache-hit == 'true' | |
| run: | | |
| echo "/opt/hostedtoolcache/singularity/${{ env.SINGULARITY_VERSION }}/x64/bin" >> $GITHUB_PATH | |
| - name: Cache singularity images | |
| id: cache-singularity-pull | |
| uses: actions/cache@v3 | |
| with: | |
| path: ${{ env.NXF_SINGULARITY_CACHEDIR }} | |
| key: ${{ runner.os }}-${{ github.sha }}--singularity | |
| - name: Pull and save singularity | |
| if: ${{ steps.cache-singularity-pull.outputs.cache-hit != 'true' }} | |
| run: | | |
| mkdir -p $NXF_SINGULARITY_CACHEDIR | |
| git grep 'ext.singularity*' conf/modules.config | cut -f 2 -d '=' | xargs -L 2 echo | tr -d ' ' > ${{ runner.temp }}/singularity_images.txt | |
| cat ${{ runner.temp }}/singularity_images.txt | sed 's/oras:\/\///;s/https:\/\///;s/\//-/g;s/$/.img/;s/:/-/' > ${{ runner.temp }}/singularity_image_paths.txt | |
| paste -d '\n' ${{ runner.temp }}/singularity_image_paths.txt ${{ runner.temp }}/singularity_images.txt | xargs -L 2 sh -c 'singularity pull --disable-cache --dir $NXF_SINGULARITY_CACHEDIR $0 $1' | |
| test: | |
| needs: [preload_docker, preload_singularity] | |
| name: Run standard workflow test | |
| if: ${{ github.event_name == 'push'}} | |
| runs-on: ubuntu-latest | |
| env: | |
| NXF_VER: ${{ matrix.nxf_ver }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| test_profile: ["test"] | |
| profile: ["docker", "singularity"] | |
| nxf_ver: ['22.10.0', ''] # minimum supported version, latest version | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@v3 | |
| - name: Install Nextflow | |
| run: | | |
| wget -qO- get.nextflow.io | bash | |
| sudo mv nextflow /usr/local/bin/ | |
| - name: Restore docker cache | |
| id: restore-docker | |
| uses: actions/cache@v3 | |
| if: matrix.profile == 'docker' | |
| with: | |
| path: ${{ runner.temp }}/docker | |
| key: ${{ runner.os }}-${{ github.sha }} | |
| - name: Load docker images from cache | |
| if: steps.restore-docker.outputs.cache-hit == 'true' | |
| run: | | |
| find $HOME -name '*.tar' | |
| find ${{ runner.temp }}/docker/ -name '*.tar' -exec sh -c 'docker load < {}' \; | |
| - name: Cache singularity setup | |
| id: restore-singularity-setup | |
| if: matrix.profile == 'singularity' | |
| uses: actions/cache@v3 | |
| with: | |
| path: /opt/hostedtoolcache/singularity/${{ env.SINGULARITY_VERSION }}/x64 | |
| key: ${{ runner.os }}-singularity-${{ env.SINGULARITY_VERSION }} | |
| - name: Add singularity to path | |
| if: steps.restore-singularity-setup.outputs.cache-hit == 'true' | |
| run: | | |
| echo "/opt/hostedtoolcache/singularity/${{ env.SINGULARITY_VERSION }}/x64/bin" >> $GITHUB_PATH | |
| - name: Restore singularity cache | |
| id: restore-singularity | |
| uses: actions/cache@v3 | |
| if: matrix.profile == 'singularity' | |
| with: | |
| path: ${{ env.NXF_SINGULARITY_CACHEDIR }} | |
| key: ${{ runner.os }}-${{ github.sha }}--singularity | |
| - name: Run pipeline with test data | |
| continue-on-error: false | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.test_profile}},${{ matrix.profile }} | |
| unit_test: | |
| needs: [preload_docker, preload_singularity] | |
| name: ${{ matrix.profile }} ${{ matrix.tags }} | |
| if: ${{ github.event_name == 'push'}} | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| profile: ["docker", "singularity"] | |
| tags: | |
| - "test input check subworkflow" | |
| - "test input check subworkflow with PGS catalog API" | |
| - "test input check subworkflow with PGS catalog API and whitespace" | |
| - "test make compatible subworkflow with bfile" | |
| - "test make compatible subworkflow with vcf" | |
| - "test make compatible subworkflow with pfile" | |
| - "test input check subworkflow with liftover 38to37" | |
| - "test input check subworkflow with liftover 37to38" | |
| - "test apply score subworkflow" | |
| - "test perfect apply score" | |
| # TODO - "test score correlation" | |
| - "test combine scorefiles module" | |
| - "test match module" | |
| - "test match combine module" | |
| - "plink2 testrelabelpvar" | |
| - "plink2 testscore" | |
| - "plink2 testsmallscore" | |
| - "plink2 testmultiscore" | |
| - "plink2 testsmallmultiscore" | |
| - "plink2 testmultiscorefail" | |
| - "plink2 vcf" | |
| - "plink2 testrelabelbim" | |
| - "pgscatalog test --pgs_id" | |
| - "pgscatalog test --efo_trait --pgp_id and --pgs_id" | |
| - "pgscatalog test bad accession" | |
| - "pgscatalog test good and bad accessions GRCh38" | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@v3 | |
| - name: Restore docker cache | |
| id: restore-docker | |
| uses: actions/cache@v3 | |
| if: matrix.profile == 'docker' | |
| with: | |
| path: ${{ runner.temp }}/docker | |
| key: ${{ runner.os }}-${{ github.sha }} | |
| - name: Load docker images from cache | |
| if: steps.restore-docker.outputs.cache-hit == 'true' | |
| run: | | |
| find $HOME -name '*.tar' | |
| find ${{ runner.temp }}/docker/ -name '*.tar' -exec sh -c 'docker load < {}' \; | |
| - name: Cache singularity setup | |
| id: cache-singularity | |
| if: matrix.profile == 'singularity' | |
| uses: actions/cache@v3 | |
| with: | |
| path: /opt/hostedtoolcache/singularity/${{ env.SINGULARITY_VERSION }}/x64 | |
| key: ${{ runner.os }}-singularity-${{ env.SINGULARITY_VERSION }} | |
| - name: Set up Singularity | |
| uses: eWaterCycle/setup-singularity@v7 | |
| if: steps.cache-singularity.outputs.cache-hit != 'true' && matrix.profile == 'singularity' | |
| - name: Add singularity to path | |
| if: steps.cache-singularity.outputs.cache-hit == 'true' && matrix.profile == 'singularity' | |
| run: | | |
| echo "/opt/hostedtoolcache/singularity/${{ env.SINGULARITY_VERSION }}/x64/bin" >> $GITHUB_PATH | |
| - name: Restore singularity cache | |
| id: restore-singularity | |
| uses: actions/cache@v3 | |
| if: matrix.profile == 'singularity' | |
| with: | |
| path: ${{ env.NXF_SINGULARITY_CACHEDIR }} | |
| key: ${{ runner.os }}-${{ github.sha }}--singularity | |
| - name: Set up Python | |
| uses: actions/setup-python@v3 | |
| with: | |
| python-version: '3.10' | |
| cache: 'pip' | |
| - run: pip install -r ${{ github.workspace }}/tests/requirements.txt | |
| - name: Install Nextflow | |
| run: | | |
| wget -qO- get.nextflow.io | bash | |
| sudo mv nextflow /usr/local/bin/ | |
| - name: Run unit tests | |
| run: TMPDIR=~ PROFILE=${{ matrix.profile }} pytest --kwdof --symlink --git-aware --wt 2 --tag "${{ matrix.tags }}" --ignore tests/bin | |
| - name: Output log on failure | |
| if: failure() | |
| run: | | |
| echo "======> log.out <=======" | |
| cat /home/runner/pytest_workflow_*/*/log.out | |
| echo | |
| echo | |
| echo "======> log.err <=======" | |
| cat /home/runner/pytest_workflow_*/*/log.err | |
| - name: Upload logs on failure | |
| if: failure() | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: logs-${{ matrix.profile }} | |
| path: | | |
| /home/runner/pytest_workflow_*/*/.nextflow.log | |
| /home/runner/pytest_workflow_*/*/log.out | |
| /home/runner/pytest_workflow_*/*/log.err | |
| /home/runner/pytest_workflow_*/*/work | |
| !/home/runner/pytest_workflow_*/*/work/conda | |
| !/home/runner/pytest_workflow_*/*/work/singularity |