convert to use umi_count #1122
Workflow file for this run
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| name: Test Singularity Build | |
| on: | |
| # push: | |
| # branches: | |
| # - master | |
| # Do the builds on all pull requests (to test them) | |
| pull_request: | |
| branches: | |
| - "*" | |
| jobs: | |
| changes: | |
| name: Checking changed files | |
| runs-on: ubuntu-latest | |
| outputs: | |
| keepgoing: ${{ steps.changed-files.outputs.any_changed }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| - name: Get changed files | |
| id: changed-files | |
| uses: tj-actions/changed-files@v41 | |
| with: | |
| files: | | |
| **/*.{yml,yaml,py} | |
| requirements.txt | |
| container/database | |
| container/tests | |
| container/scripts/*.{sh,py} | |
| container/*.{yml,yaml,py,def} | |
| tests | |
| - name: List all changed files | |
| run: | | |
| for file in ${{ steps.changed-files.outputs.all_changed_files }}; do | |
| echo "$file was changed" | |
| done | |
| echo ${{ steps.changed-files.outputs.any_changed }} | |
| container: | |
| needs: | |
| - changes | |
| if: needs.changes.outputs.keepgoing == 'true' | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Check out code for the container build | |
| uses: actions/checkout@v3 | |
| - name: Setup Singularity | |
| uses: singularityhub/install-singularity@main | |
| - name: Extract repository location | |
| shell: bash | |
| run: | | |
| echo "location=$(echo " - git+https://www.github.com/${GITHUB_REPOSITORY}@${GITHUB_REF#refs/heads/}")" >> $GITHUB_OUTPUT | |
| id: extract_location | |
| - name: Build Container | |
| run: | | |
| cd container | |
| echo '${{ steps.extract_location.outputs.location }}' >> environment_test.yml | |
| sudo -E singularity build --notest sc-dandelion.sif sc-dandelion_test.def | |
| - name: Test Container | |
| run: | | |
| cd container | |
| sudo singularity test --writable-tmpfs sc-dandelion.sif | |
| singularity run -B $PWD sc-dandelion.sif dandelion-preprocess --help |