github-action-rna-seq-pop-paired-end.yml

name: rna-seq-pop-paired-end

on: pull_request

jobs:
  run-workflow:
    runs-on: ubuntu-latest
    steps:
      - name: Set up python3
        uses: actions/setup-python@v2
        with:
          python-version: '3.9' # Version range or exact version of a Python version to use, using SemVer's version range syntax

      - name: Checkout repository
        uses: actions/checkout@v2
        with:
          submodules: recursive
        
      - name: cp pfam/go files
        run: cp resources/Anogam_long.pep_eggnog_diamond.emapper.annotations.tsv.gz resources/Anogam_long.pep_Pfamscan.seqs.gz .test/resources

      - name: cp results book yamls 
        run: cp docs/rna-seq-pop-results/_toc.yml docs/rna-seq-pop-results/_config.yml .test/docs/rna-seq-pop-results

      - name: Test workflow paired-end
        uses: snakemake/snakemake-github-action@v1.23.0
        with:
          directory: '.test'
          snakefile: 'workflow/Snakefile'
          args: '--cores 4 --use-conda --configfile .test/config/config_paired_end.yaml --conda-cleanup-pkgs cache'