dry-run.yaml

name: latest-dry-run
on: workflow_dispatch

env:
  COMPAREM2_PROFILE: "profile/conda/default"


jobs:
  create-env:
    name: ${{ matrix.os }} 
    runs-on: ${{ matrix.os }}
    defaults:
      run:
        shell: bash -l {0}
        
    strategy:
      fail-fast: false
      matrix:
        os: [ubuntu-latest]
        
    steps:
      - name: checkout repository
        uses: actions/checkout@v2
        
      - name: create environment with mamba
        uses: conda-incubator/setup-miniconda@v2
        with:
          mamba-version: "<2"
          channels: conda-forge,bioconda,defaults
          auto-activate-base: false
          activate-environment: comparem2_launcher
          environment-file: environment.yaml
      
      - name: check solution
        run: |
          mamba env export
      
      - name: test installation
        run: |
          python --version
          snakemake --version
          ./comparem2 --help
          ./comparem2 --version
          ./comparem2 --cite
          ./comparem2 --status
          


      - name: dry run
        run: |
          ./comparem2 --dry-run
          rm -rf .snakemake results_comparem2

          ./comparem2 --until metadata
          rm -rf .snakemake results_comparem2
          
          touch dummy_1.fa; ./comparem2 --dry-run
          touch dummy_2.fa; ./comparem2 --dry-run
          touch dummy_3.fa; ./comparem2 --dry-run
          
          
          unzip tests/E._faecium/fna.zip
          ./comparem2 --config input_genomes="*.fna" --dry-run
          ./comparem2 --config input_genomes="*.fna" --until fast --dry-run
          ./comparem2 --config input_genomes="*.fna" --until isolate --dry-run
          ./comparem2 --config input_genomes="*.fna" --until meta --dry-run
          ./comparem2 --config input_genomes="*.fna" --until downloads --dry-run
          
          ls dummy_{2,3}.fa > fofn.txt; ./comparem2 --config fofn="fofn.txt" --dry-run