main.yaml

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_dry
        shell: bash -l {0}
        run: |
          snakemake -npr --configfile .test/config/config_snpeff_gerp.yaml -j 4 --cores 1 --use-singularity

      - name: snpeff_gerp
        shell: bash -l {0}
        run: |
          snakemake --configfile .test/config/config_snpeff_gerp.yaml -j 4 --cores 1 --use-singularity