mitogenome_mapping.yaml

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