Optional removal of sex chromosomes from VCF files #65
Workflow file for this run
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| name: CI | |
| on: | |
| push: | |
| paths-ignore: | |
| - 'README.md' | |
| - 'LICENSE.md' | |
| branches: | |
| - main | |
| pull_request: | |
| paths-ignore: | |
| - 'README.md' | |
| - 'LICENSE.md' | |
| - 'workflow/docker' | |
| 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: mitogenome_mapping_dry | |
| shell: bash -l {0} | |
| run: | | |
| snakemake -npr --configfile .test/config/config_mitogenomes.yaml -j 4 --cores 1 --use-singularity | |
| - name: mitogenome_mapping | |
| shell: bash -l {0} | |
| run: | | |
| snakemake --configfile .test/config/config_mitogenomes.yaml -j 4 --cores 1 --use-singularity | |
| - name: mlRho_options_dry | |
| shell: bash -l {0} | |
| run: | | |
| snakemake -npr --configfile .test/config/config_mlRho_options.yaml -j 4 --cores 1 --use-singularity | |
| - name: mlRho_options | |
| shell: bash -l {0} | |
| run: | | |
| snakemake --configfile .test/config/config_mlRho_options.yaml -j 4 --cores 1 --use-singularity | |
| - name: pca_roh_dry | |
| shell: bash -l {0} | |
| run: | | |
| snakemake -npr --configfile .test/config/config_pca_roh.yaml -j 4 --cores 1 --use-singularity | |
| - name: pca_roh | |
| shell: bash -l {0} | |
| run: | | |
| snakemake --configfile .test/config/config_pca_roh.yaml -j 4 --cores 1 --use-singularity | |
| - name: snpeff_gerp_autos_dry | |
| shell: bash -l {0} | |
| run: | | |
| snakemake -npr --configfile .test/config/config_snpeff_gerp_autos.yaml -j 4 --cores 1 --use-singularity | |
| - name: snpeff_gerp_autos | |
| shell: bash -l {0} | |
| run: | | |
| snakemake --configfile .test/config/config_snpeff_gerp_autos.yaml -j 4 --cores 1 --use-singularity |