snpeff.yaml

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@v4
      
      - uses: eWaterCycle/setup-apptainer@v2
        with:
          apptainer-version: 1.3.5

      - uses: conda-incubator/setup-miniconda@v3
        with:
          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