Fix bugs in the GERP step of the pipeline #88
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| name: mitogenome_mapping | |
| on: | |
| push: | |
| paths-ignore: | |
| - 'README.md' | |
| - 'LICENSE.md' | |
| - 'workflow/rules/0.1_reference_genome_preps.smk' | |
| - 'workflow/rules/0.2_repeat_identification.smk' | |
| - 'workflow/rules/2_mapping.smk' | |
| - 'workflow/rules/3.1_bam_rmdup_realign_indels.smk' | |
| - 'workflow/rules/3.2_historical_bam_mapDamage.smk' | |
| - 'workflow/rules/3.3_bam_subsampling.smk' | |
| - 'workflow/rules/4_genotyping.smk' | |
| - 'workflow/rules/5_CpG_identification.smk' | |
| - 'workflow/rules/6_autosome_sexchromosome_bed_files.smk' | |
| - 'workflow/rules/7_mlRho.smk' | |
| - 'workflow/rules/8.1_vcf_CpG_filtering.smk' | |
| - 'workflow/rules/8.2_vcf_qual_repeat_filtering.smk' | |
| - 'workflow/rules/9_merge_vcfs.smk' | |
| - 'workflow/rules/10_pca.smk' | |
| - 'workflow/rules/11_ROH.smk' | |
| - 'workflow/rules/12_snpEff.smk' | |
| - 'workflow/rules/13_GERP.smk' | |
| branches: | |
| - main | |
| pull_request: | |
| paths-ignore: | |
| - 'README.md' | |
| - 'LICENSE.md' | |
| - 'workflow/docker' | |
| - 'workflow/rules/0.1_reference_genome_preps.smk' | |
| - 'workflow/rules/0.2_repeat_identification.smk' | |
| - 'workflow/rules/2_mapping.smk' | |
| - 'workflow/rules/3.1_bam_rmdup_realign_indels.smk' | |
| - 'workflow/rules/3.2_historical_bam_mapDamage.smk' | |
| - 'workflow/rules/3.3_bam_subsampling.smk' | |
| - 'workflow/rules/4_genotyping.smk' | |
| - 'workflow/rules/5_CpG_identification.smk' | |
| - 'workflow/rules/6_autosome_sexchromosome_bed_files.smk' | |
| - 'workflow/rules/7_mlRho.smk' | |
| - 'workflow/rules/8.1_vcf_CpG_filtering.smk' | |
| - 'workflow/rules/8.2_vcf_qual_repeat_filtering.smk' | |
| - 'workflow/rules/9_merge_vcfs.smk' | |
| - 'workflow/rules/10_pca.smk' | |
| - 'workflow/rules/11_ROH.smk' | |
| - 'workflow/rules/12_snpEff.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: mitogenome_mapping_dry | |
| shell: bash -l {0} | |
| run: | | |
| snakemake -np -k --configfile .test/config/config_mitogenomes.yaml -j 4 --cores 1 --use-singularity | |
| - name: mitogenome_mapping | |
| shell: bash -l {0} | |
| run: | | |
| snakemake -k --configfile .test/config/config_mitogenomes.yaml -j 4 --cores 1 --use-singularity | |