Enable download of FASTQ files from NCBI/ENA when an SRA accession is supplied #136
Workflow file for this run
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| name: Tests | |
| on: | |
| push: | |
| branches: | |
| - master | |
| paths-ignore: | |
| - '**/*.md' | |
| pull_request: | |
| branches_ignore: [] | |
| paths-ignore: | |
| - '**/*.md' | |
| jobs: | |
| formatting: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout with submodules | |
| uses: actions/checkout@v3.5.2 | |
| - name: Formatting | |
| uses: github/super-linter@v5 | |
| env: | |
| VALIDATE_ALL_CODEBASE: false | |
| DEFAULT_BRANCH: master | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| VALIDATE_SNAKEMAKE_SNAKEFMT: true | |
| linting: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3.5.2 | |
| - name: Linting | |
| uses: snakemake/snakemake-github-action@v1.24.0 | |
| with: | |
| snakefile: "workflow/Snakefile" | |
| args: "--lint" | |
| run-workflow: | |
| runs-on: ubuntu-latest | |
| needs: | |
| - linting | |
| - formatting | |
| steps: | |
| - name: Maximize build space | |
| uses: easimon/maximize-build-space@master | |
| with: | |
| root-reserve-mb: 1024 | |
| swap-size-mb: 1024 | |
| overprovision-lvm: 'true' | |
| remove-dotnet: 'true' | |
| remove-android: 'true' | |
| remove-haskell: 'true' | |
| remove-codeql: 'true' | |
| remove-docker-images: 'true' | |
| - name: Checkout repository | |
| uses: actions/checkout@v3.5.2 | |
| - name: Set up conda environment and singularity | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-file: environment.yaml | |
| create-args: >- | |
| apptainer | |
| - name: Test workflow | |
| shell: bash -l {0} | |
| run: | | |
| mkdir -p temp | |
| workdir=$(pwd -P) | |
| TMPDIR=$workdir/temp | |
| snakemake --directory .test --configfile .test/config/config.yaml --config samples=config/samples_testSRA.tsv --use-conda --show-failed-logs --cores 2 --conda-cleanup-pkgs cache --use-singularity --default-resources mem_mb=1000 --until fastp_mergedout | |
| snakemake --directory .test --configfile .test/config/config.yaml --use-conda --show-failed-logs --cores 2 --conda-cleanup-pkgs cache --use-singularity --default-resources mem_mb=1000 | |
| - name: Test report | |
| shell: bash -l {0} | |
| run: | | |
| snakemake --directory .test --configfile .test/config/config.yaml --cores 2 --report report.html |