Update so that apptainer correctly binds the directory with input data #64
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| name: snpeff | |
| on: | |
| push: | |
| paths-ignore: | |
| - 'README.md' | |
| - 'LICENSE.md' | |
| - 'workflow/rules/1.2_map_to_mitogenomes.smk' | |
| - 'workflow/rules/7_mlRho.smk' | |
| - 'workflow/rules/10_pca.smk' | |
| - 'workflow/rules/11_ROH.smk' | |
| - 'workflow/rules/13_GERP.smk' | |
| branches: | |
| - main | |
| pull_request: | |
| paths-ignore: | |
| - 'README.md' | |
| - 'LICENSE.md' | |
| - 'workflow/docker' | |
| - 'workflow/rules/1.2_map_to_mitogenomes.smk' | |
| - 'workflow/rules/7_mlRho.smk' | |
| - 'workflow/rules/10_pca.smk' | |
| - 'workflow/rules/11_ROH.smk' | |
| - 'workflow/rules/13_GERP.smk' | |
| branches: | |
| - main | |
| - dev | |
| jobs: | |
| test: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: eWaterCycle/setup-apptainer@v2 | |
| with: | |
| apptainer-version: 1.1.4 | |
| - uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| miniforge-variant: Mambaforge | |
| channels: conda-forge,bioconda | |
| activate-environment: generode | |
| environment-file: environment.yml | |
| auto-activate-base: false | |
| - name: conda_environment | |
| shell: bash -l {0} | |
| run: | | |
| conda info | |
| conda list | |
| - name: Free Up GitHub Actions Ubuntu Runner Disk Space 🔧 | |
| uses: jlumbroso/free-disk-space@main | |
| 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 | |
| swap-storage: true | |
| - name: snpeff_dry | |
| shell: bash -l {0} | |
| run: | | |
| snakemake -np -k --configfile .test/config/config_snpeff.yaml -j 4 --cores 1 --use-singularity | |
| - name: snpeff | |
| shell: bash -l {0} | |
| run: | | |
| snakemake -k --configfile .test/config/config_snpeff.yaml -j 4 --cores 1 --use-singularity |