feat: add option to allow mapping to pangenome #1895
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| name: Tests | |
| on: | |
| push: | |
| branches: [ master ] | |
| pull_request: | |
| branches_ignore: [] | |
| jobs: | |
| Formatting: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| with: | |
| # Full git history is needed to get a proper | |
| # list of changed files within `super-linter` | |
| fetch-depth: 0 | |
| - 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@v2 | |
| with: | |
| fetch-depth: 0 | |
| - name: Lint workflow | |
| uses: snakemake/snakemake-github-action@v1 | |
| with: | |
| directory: . | |
| snakefile: workflow/Snakefile | |
| stagein: "mamba install -y -n snakemake --channel conda-forge pyarrow=6.0" | |
| args: "--lint" | |
| Dryrun_Tests: | |
| runs-on: ubuntu-latest | |
| needs: | |
| - Linting | |
| - Formatting | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Test workflow (local FASTQs) | |
| uses: snakemake/snakemake-github-action@v1 | |
| with: | |
| directory: .test | |
| snakefile: workflow/Snakefile | |
| args: "--configfile .test/config-simple/config.yaml --use-conda --show-failed-logs -j 10 --conda-cleanup-pkgs cache --dryrun" | |
| show-disk-usage-on-error: true | |
| - name: Test testcase generation | |
| uses: snakemake/snakemake-github-action@v1 | |
| with: | |
| directory: .test | |
| snakefile: workflow/Snakefile | |
| args: "results/testcases/one/freebayes/IX:314200 --configfile .test/config-simple/config.yaml --use-conda --show-failed-logs -j 10 --conda-cleanup-pkgs cache --dryrun" | |
| show-disk-usage-on-error: true | |
| - name: Test workflow (local FASTQs, target regions) | |
| uses: snakemake/snakemake-github-action@v1 | |
| with: | |
| directory: .test | |
| snakefile: workflow/Snakefile | |
| args: "--configfile .test/config-target-regions/config.yaml --use-conda --show-failed-logs -j 10 --conda-cleanup-pkgs cache --dryrun" | |
| show-disk-usage-on-error: true | |
| - name: Test workflow (local FASTQs, multiple target regions BED files) | |
| uses: snakemake/snakemake-github-action@v1 | |
| with: | |
| directory: .test | |
| snakefile: workflow/Snakefile | |
| args: "--configfile .test/config-target-regions/config_multiple_beds.yaml --use-conda --show-failed-logs -j 10 --conda-cleanup-pkgs cache --dryrun" | |
| show-disk-usage-on-error: true | |
| - name: Test workflow (local FASTQs, no candidate filtering) | |
| uses: snakemake/snakemake-github-action@v1 | |
| with: | |
| directory: .test | |
| snakefile: workflow/Snakefile | |
| args: "--configfile .test/config-no-candidate-filtering/config.yaml --use-conda --show-failed-logs -j 10 --conda-cleanup-pkgs cache --dryrun" | |
| show-disk-usage-on-error: true | |
| - name: Test workflow (local FASTQs primer) | |
| uses: snakemake/snakemake-github-action@v1 | |
| with: | |
| directory: .test | |
| snakefile: workflow/Snakefile | |
| args: "--configfile .test/config_primers/config.yaml --use-conda --show-failed-logs -j 10 --conda-cleanup-pkgs cache --dryrun" | |
| show-disk-usage-on-error: true | |
| - name: Test workflow (SRA FASTQs) | |
| uses: snakemake/snakemake-github-action@v1 | |
| with: | |
| directory: .test | |
| snakefile: workflow/Snakefile | |
| args: "--configfile .test/config-sra/config.yaml --show-failed-logs --use-conda --cores all --set-scatter calling=4 --conda-cleanup-pkgs cache --dryrun" | |
| show-disk-usage-on-error: true | |
| Quick_Tests: | |
| runs-on: ubuntu-latest | |
| needs: | |
| - Dryrun_Tests | |
| steps: | |
| - name: update apt | |
| run: sudo apt-get update | |
| - name: Free Disk Space (Ubuntu) | |
| uses: jlumbroso/[email protected] | |
| with: | |
| # this might remove tools that are actually needed, | |
| # if set to "true" but frees about 6 GB | |
| tool-cache: false | |
| # all of these default to true, but feel free to set to | |
| # "false" if necessary for your workflow | |
| android: true | |
| dotnet: true | |
| haskell: true | |
| large-packages: true | |
| docker-images: false | |
| swap-storage: true | |
| - uses: actions/checkout@v2 | |
| - name: Test workflow (local FASTQs) | |
| uses: snakemake/snakemake-github-action@v1 | |
| with: | |
| directory: .test | |
| snakefile: workflow/Snakefile | |
| args: "--configfile .test/config-simple/config.yaml --use-conda --show-failed-logs -j 10 --conda-cleanup-pkgs cache" | |
| show-disk-usage-on-error: true | |
| - name: Test testcase generation | |
| uses: snakemake/snakemake-github-action@v1 | |
| with: | |
| directory: .test | |
| snakefile: workflow/Snakefile | |
| args: "results/testcases/one/freebayes/IX:314200 --configfile .test/config-simple/config.yaml --use-conda --show-failed-logs -j 10 --conda-cleanup-pkgs cache" | |
| show-disk-usage-on-error: true | |
| - name: Test report | |
| uses: snakemake/snakemake-github-action@v1 | |
| with: | |
| directory: .test | |
| snakefile: workflow/Snakefile | |
| args: "--configfile .test/config-simple/config.yaml --cores 1 --report report.zip" | |
| show-disk-usage-on-error: true | |
| - name: Test workflow (local FASTQs, target regions) | |
| uses: snakemake/snakemake-github-action@v1 | |
| with: | |
| directory: .test | |
| snakefile: workflow/Snakefile | |
| args: "--configfile .test/config-target-regions/config.yaml --use-conda --show-failed-logs -j 10 --conda-cleanup-pkgs cache" | |
| stagein: | | |
| rm -rf .test/results | |
| show-disk-usage-on-error: true | |
| - name: Test workflow (local FASTQs, multiple target regions BED files) | |
| uses: snakemake/snakemake-github-action@v1 | |
| with: | |
| directory: .test | |
| snakefile: workflow/Snakefile | |
| args: "--configfile .test/config-target-regions/config_multiple_beds.yaml --use-conda --show-failed-logs -j 10 --conda-cleanup-pkgs cache" | |
| stagein: | | |
| rm -rf .test/results | |
| show-disk-usage-on-error: true | |
| - name: Test workflow (local FASTQs, no candidate filtering) | |
| uses: snakemake/snakemake-github-action@v1 | |
| with: | |
| directory: .test | |
| snakefile: workflow/Snakefile | |
| args: "--configfile .test/config-no-candidate-filtering/config.yaml --use-conda --show-failed-logs -j 10 --conda-cleanup-pkgs cache" | |
| stagein: | | |
| rm -rf .test/results | |
| show-disk-usage-on-error: true | |
| - name: Test workflow (local FASTQs primer) | |
| uses: snakemake/snakemake-github-action@v1 | |
| with: | |
| directory: .test | |
| snakefile: workflow/Snakefile | |
| args: "--configfile .test/config_primers/config.yaml --use-conda --show-failed-logs -j 10 --conda-cleanup-pkgs cache" | |
| stagein: | | |
| rm -rf .test/results | |
| show-disk-usage-on-error: true | |
| Long_Tests: | |
| runs-on: ubuntu-latest | |
| needs: | |
| - Dryrun_Tests | |
| steps: | |
| - name: update apt | |
| run: sudo apt-get update | |
| - name: Free Disk Space (Ubuntu) | |
| uses: jlumbroso/[email protected] | |
| with: | |
| # this might remove tools that are actually needed, | |
| # if set to "true" but frees about 6 GB | |
| tool-cache: false | |
| # all of these default to true, but feel free to set to | |
| # "false" if necessary for your workflow | |
| android: true | |
| dotnet: true | |
| haskell: true | |
| large-packages: true | |
| docker-images: false | |
| swap-storage: true | |
| - uses: actions/checkout@v2 | |
| - name: Test workflow (SRA FASTQs) | |
| uses: snakemake/snakemake-github-action@v1 | |
| with: | |
| directory: .test | |
| snakefile: workflow/Snakefile | |
| args: "--configfile .test/config-sra/config.yaml --show-failed-logs --use-conda --cores all --set-scatter calling=4 --conda-cleanup-pkgs cache" | |
| show-disk-usage-on-error: true |