lintr.yaml

name: lintr
on:
  push:
    branches:
      - master
      - dev
  pull_request:
    branches:
      - master
      - dev

jobs:
  Lintr:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v2
      - uses: docker://snakemake/snakemake:v7.19.1
      - name: Lint 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.'"