CI.yml

name: CI

on:
  push:
    branches:
      - '**'
    paths-ignore:
      - '*.md'
      - '*.ignore'
      - LICENSE
      - Dockerfile      # as we build and push manually right now
      - environment.yml # as we build and push manually right now

jobs:
  
  atac_chip_preprocess_ci:
    
    runs-on: ubuntu-latest

    steps:

      - uses: actions/checkout@v2

      - name: INSTALL-NEXTFLOW
        run: |
          wget -qO- get.nextflow.io | bash
          sudo mv nextflow /usr/local/bin/

      - name: TEST-DOCKER-ATACseq
        run: |
          NXF_VER=23.04.0 nextflow run main.nf -profile test,docker --keep_merge --keep_trim
          
      - name: Commit software versions
        run: |
          git config --global user.name 'atpoint'
          git config --global user.email 'atpoint@users.noreply.github.com'
          mkdir -p misc && cp atac_chip_preprocess_results/pipeline_info/*.txt misc/
          git add misc/*.txt
          if (( $(git status -s | grep -c 'misc/') > 0 )); then 
            git commit -am "update software version and command line reports"
            git push -f
          fi

      - name: TEST-DOCKER-ChIPseq
        run: |
          NXF_VER=23.04.0 nextflow run main.nf -profile test,docker --keep_merge --keep_trim --atacseq false --macs_additional '\--keep-dup=all --nomodel --extsize 150'