main.yaml

name: tests

on:
  workflow_dispatch:
  push:
    branches:
      - master
      - main
  pull_request:
    branches_ignore: []

jobs:
  Dry_Run_and_Lint_DNA_RNA:
    runs-on: ubuntu-latest
    steps:
    - uses: actions/checkout@v2
    - uses: docker://snakemake/snakemake:latest
    - name: Dry Run 
      run: |
        docker run -v $PWD:/opt2 snakemake/snakemake:latest \
        /opt2/metamorph run --input /opt2/.tests/test_cohort.txt \
        --output /opt2/output --mode local --dry-run
    - name: View the pipeline config file [DNA & RNA modes]
      run: |
        echo "Generated config file for pipeline...." && cat $PWD/output/config.json
    - name: Lint Workflow
      continue-on-error: true
      run: |
        docker run -v $PWD:/opt2 snakemake/snakemake:latest snakemake --lint -s /opt2/output/workflow/Snakefile -d /opt2/output || \
        echo 'There may have been a few warnings or errors. Please read through the log to determine if its harmless.'
  Dry_Run_and_Lint_DNAonly1:
    runs-on: ubuntu-latest
    steps:
    - uses: actions/checkout@v2
    - uses: docker://snakemake/snakemake:latest
    - name: Dry Run [DNA only mode]
      run: |
        docker run -v $PWD:/opt2 snakemake/snakemake:latest \
        /opt2/metamorph run --input /opt2/.tests/test_cohort_DNAonly.txt \
        --output /opt2/output --mode local --dry-run
    - name: View the pipeline config file [DNA only mode]
      run: |
        echo "Generated config file for pipeline...." && cat $PWD/output/config.json
    - name: Lint Workflow
      continue-on-error: true
      run: |
        docker run -v $PWD:/opt2 snakemake/snakemake:latest snakemake --lint -s /opt2/output/workflow/Snakefile -d /opt2/output || \
        echo 'There may have been a few warnings or errors. Please read through the log to determine if its harmless.'
  Dry_Run_DNA2:
    runs-on: ubuntu-latest
    steps:
    - uses: actions/checkout@v2
    - uses: docker://snakemake/snakemake:latest
    - name: Dry Run [DNA only mode w RNA column]
      run: |
        docker run -v $PWD:/opt2 snakemake/snakemake:latest \
        /opt2/metamorph run --input /opt2/.tests/test_cohort_DNAonly_RNAcolexists.txt \
        --output /opt2/output --mode local --dry-run