Fix bugs in the GERP step of the pipeline #95
Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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 |