Workflow file for this run
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| name: Run ancestry test with singularity or docker profiles | ||
| on: | ||
| workflow_call: | ||
| inputs: | ||
| container-cache-key: | ||
| type: string | ||
| required: true | ||
| ancestry-cache-key: | ||
| type: string | ||
| required: true | ||
| docker: | ||
| type: boolean | ||
| singularity: | ||
| type: boolean | ||
| env: | ||
| NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/singularity | ||
| SINGULARITY_VERSION: 3.8.3 | ||
| jobs: | ||
| docker: | ||
| if: ${{ inputs.docker }} | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - name: Set environment variables | ||
| run: | | ||
| echo "ANCESTRY_REF_DIR=$RUNNER_TEMP" >> $GITHUB_ENV | ||
| echo "ANCESTRY_TARGET_DIR=$RUNNER_TEMP" >> $GITHUB_ENV | ||
| - name: Check out pipeline code | ||
| uses: actions/checkout@v3 | ||
| - uses: nf-core/setup-nextflow@v1 | ||
| - name: Restore docker images | ||
| id: restore-docker | ||
| uses: actions/cache/restore@v3 | ||
| with: | ||
| path: ${{ runner.temp }}/docker | ||
| key: ${{ inputs.container-cache-key }} | ||
| fail-on-cache-miss: true | ||
| - name: Load docker images from cache | ||
| run: | | ||
| find $HOME -name '*.tar' | ||
| find ${{ runner.temp }}/docker/ -name '*.tar' -exec sh -c 'docker load < {}' \; | ||
| - name: Restore reference data | ||
| uses: actions/cache/restore@v3 | ||
| with: | ||
| path: | | ||
| ${{ env.ANCESTRY_TARGET_DIR }}/GRCh38_HAPNEST_TARGET_ALL.pgen | ||
| ${{ env.ANCESTRY_TARGET_DIR }}/GRCh38_HAPNEST_TARGET_ALL.psam | ||
| ${{ env.ANCESTRY_TARGET_DIR }}/GRCh38_HAPNEST_TARGET_ALL.pvar.zst | ||
| ${{ env.ANCESTRY_REF_DIR }}/GRCh38_HAPNEST_reference.tar.zst | ||
| key: ${{ inputs.ancestry-cache-key }} | ||
| fail-on-cache-miss: true | ||
| - name: Install plink2 to recode | ||
| run: sudo apt-get install -y plink2 | ||
| - name: run plink2 | ||
| run: | | ||
| plink2 --pfile ${ANCESTRY_TARGET_DIR}/GRCh38_HAPNEST_TARGET_ALL vzs \ | ||
| --export vcf bgz \ | ||
| --out ${ANCESTRY_TARGET_DIR}/GRCh38_HAPNEST_TARGET_ALL | ||
| - name: Set up test requirements | ||
| uses: actions/setup-python@v3 | ||
| with: | ||
| python-version: '3.10' | ||
| cache: 'pip' | ||
| - run: pip install -r ${{ github.workspace }}/tests/requirements.txt | ||
| - name: Run ancestry test | ||
| run: TMPDIR=~ PROFILE=docker pytest --kwdof --symlink --git-aware --wt 2 --tag "ancestry vcf" --ignore tests/bin | ||
| - name: Upload logs on failure | ||
| if: failure() | ||
| uses: actions/upload-artifact@v3 | ||
| with: | ||
| name: logs-singularity-ancestry | ||
| path: | | ||
| /home/runner/pytest_workflow_*/*/.nextflow.log | ||
| /home/runner/pytest_workflow_*/*/log.out | ||
| /home/runner/pytest_workflow_*/*/log.err | ||
| /home/runner/pytest_workflow_*/*/output/* | ||
| singularity: | ||
| if: ${{ inputs.singularity }} | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - name: Set environment variables | ||
| run: | | ||
| echo "ANCESTRY_REF_DIR=$RUNNER_TEMP" >> $GITHUB_ENV | ||
| echo "ANCESTRY_TARGET_DIR=$RUNNER_TEMP" >> $GITHUB_ENV | ||
| - name: Check out pipeline code | ||
| uses: actions/checkout@v3 | ||
| - uses: nf-core/setup-nextflow@v1 | ||
| - name: Restore singularity setup | ||
| id: restore-singularity-setup | ||
| uses: actions/cache@v3 | ||
| with: | ||
| path: /opt/hostedtoolcache/singularity/${{ env.SINGULARITY_VERSION }}/x64 | ||
| key: ${{ runner.os }}-singularity-${{ env.SINGULARITY_VERSION }} | ||
| fail-on-cache-miss: true | ||
| - name: Add singularity to path | ||
| run: | | ||
| echo "/opt/hostedtoolcache/singularity/${{ env.SINGULARITY_VERSION }}/x64/bin" >> $GITHUB_PATH | ||
| - name: Restore singularity container images | ||
| id: restore-singularity | ||
| uses: actions/cache@v3 | ||
| with: | ||
| path: ${{ env.NXF_SINGULARITY_CACHEDIR }} | ||
| key: ${{ inputs.container-cache-key }} | ||
| - name: Restore reference data | ||
| uses: actions/cache/restore@v3 | ||
| with: | ||
| path: | | ||
| ${{ env.ANCESTRY_TARGET_DIR }}/GRCh38_HAPNEST_TARGET_ALL.pgen | ||
| ${{ env.ANCESTRY_TARGET_DIR }}/GRCh38_HAPNEST_TARGET_ALL.psam | ||
| ${{ env.ANCESTRY_TARGET_DIR }}/GRCh38_HAPNEST_TARGET_ALL.pvar.zst | ||
| ${{ env.ANCESTRY_REF_DIR }}/GRCh38_HAPNEST_reference.tar.zst | ||
| key: ${{ inputs.ancestry-cache-key }} | ||
| fail-on-cache-miss: true | ||
| - name: Set up test requirements | ||
| uses: actions/setup-python@v3 | ||
| with: | ||
| python-version: '3.10' | ||
| cache: 'pip' | ||
| - run: pip install -r ${{ github.workspace }}/tests/requirements.txt | ||
| - name: Run ancestry test | ||
| run: TMPDIR=~ PROFILE=singularity pytest --kwdof --symlink --git-aware --wt 2 --tag "ancestry" --ignore tests/bin | ||
| - name: Upload logs on failure | ||
| if: failure() | ||
| uses: actions/upload-artifact@v3 | ||
| with: | ||
| name: logs-singularity-ancestry | ||
| path: | | ||
| /home/runner/pytest_workflow_*/*/.nextflow.log | ||
| /home/runner/pytest_workflow_*/*/log.out | ||
| /home/runner/pytest_workflow_*/*/log.err | ||
| /home/runner/pytest_workflow_*/*/output/* | ||
