test_dev.yml

name: DevTesting
on:
  push:
    branches:
      - dev
jobs:
  deploy:
    runs-on: ubuntu-latest
    steps:
    - uses: docker://snakemake/snakemake:v7.19.1
      with:
        directory: '.test'
        snakefile: 'workflow/Snakefile'
        args: '--cores 1 --use-conda --conda-cleanup-pkgs cache'
        stagein: '' # additional preliminary commands to run (can be multiline)

    - name: Dev Testing Workflow
      continue-on-error: true
      run: |
        docker run -v $PWD:/opt2 snakemake/snakemake:v7.19.1 /bin/bash -c \
          "mkdir -p /opt2/output_carlisle/config /opt2/output_carlisle/annotation && \
          cp -r /opt2/workflow/scripts/ /opt2/output_carlisle/ && \
          cp /opt2/resources/cluster_biowulf.yaml /opt2/output_carlisle/config/cluster.yaml && \
          cp /opt2/resources/tools_biowulf.yaml /opt2/output_carlisle/config/tools.yaml && \
          cd /opt2/output_carlisle/annotation && \
          touch hg38.fa genes.gtf hg38.bed hg38.tss.bed hg38_refseq.ucsc Ecoli_GCF_000005845.2_ASM584v2_genomic.fna adapters.fa && \
          snakemake --lint -s /opt2/workflow/Snakefile \
          -d /opt2/output_carlisle --configfile /opt2/.test/config_lint.yaml || \
          echo 'There may have been a few warnings or errors. Please read through the log to determine if its harmless.'"