feat: Allow bam input files #611
Workflow file for this run
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| #name: My build action requiring more space | |
| #on: push | |
| # | |
| #jobs: | |
| # build: | |
| # name: Build my artifact | |
| # runs-on: ubuntu-latest | |
| # steps: | |
| # - name: Maximize build space | |
| # uses: easimon/maximize-build-space@master | |
| # with: | |
| # root-reserve-mb: 512 | |
| # swap-size-mb: 1024 | |
| # remove-dotnet: 'true' | |
| # remove-android: 'true' | |
| # remove-haskell: 'true' | |
| # - name: Checkout | |
| # uses: actions/checkout@v2 | |
| # | |
| # - name: Build | |
| # run: | | |
| # echo "Free space:" | |
| # df -h | |
| # echo "free space in ${{ github.workspace }}" | |
| # du -hs $(ls -A) ${{ github.workspace }}/* | |
| # rm -rf ${{ github.workspace }}/* | |
| # echo "free space in .test" | |
| # du -hs $(ls -A) .test/* | |
| name: Tests | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| branches_ignore: [] | |
| jobs: | |
| formatting: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Formatting | |
| uses: github/super-linter@v5 | |
| env: | |
| VALIDATE_ALL_CODEBASE: false | |
| DEFAULT_BRANCH: main | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| VALIDATE_SNAKEMAKE_SNAKEFMT: true | |
| linting: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Linting | |
| uses: snakemake/snakemake-github-action@v1 | |
| with: | |
| directory: .test | |
| snakefile: workflow/Snakefile | |
| args: "--lint" | |
| run-rna-workflow: | |
| runs-on: ubuntu-latest | |
| needs: | |
| - linting | |
| - formatting | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v3 | |
| with: | |
| submodules: recursive | |
| - name: Test workflow | |
| uses: snakemake/snakemake-github-action@v1 | |
| with: | |
| directory: .test | |
| snakefile: workflow/Snakefile | |
| args: "--use-conda --show-failed-logs --cores all --conda-cleanup-pkgs cache --all-temp" | |
| run-three-prime-rna-workflow: | |
| runs-on: ubuntu-latest | |
| needs: | |
| - linting | |
| - formatting | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v3 | |
| - name: Test 3-prime-workflow | |
| uses: snakemake/snakemake-github-action@v1 | |
| with: | |
| directory: .test/three_prime | |
| snakefile: .test/three_prime/workflow/Snakefile | |
| args: "--use-conda --show-failed-logs --cores all --conda-cleanup-pkgs cache --all-temp" | |
| # Disable report testing for now since we mark all output files as temporary above. | |
| # TODO: add some kind of test mode to report generation which does not really try to include | |
| # results. | |
| # - name: Test report | |
| # uses: snakemake/snakemake-github-action@v1 | |
| # with: | |
| # directory: .test | |
| # snakefile: workflow/Snakefile | |
| # args: "--report report.zip" |