diff_check.yml

name: diff_check
on:
  push:

jobs:
  concordance-test:
    runs-on: ubuntu-latest
    steps:
      - name: Checkout Repository
        uses: actions/checkout@v2
      - name: Check
        run: |
          EXITCODE=0
          for subdir in warden_bam/resources/app_data/internal_source/*; do
            if [ "$(basename "$subdir")" = "warden_genome_coverage_bed" ]; then
              continue
            fi
            echo "Checking WARDEN (BAM): $(basename "$subdir")"
            result=$(diff -r -q "$subdir" warden_fastq/resources/app_data/internal_source/"$(basename "$subdir")") || true
            if [[ -n "$result" ]]; then
              echo "$result"
              EXITCODE=1
            fi
          done
          for subdir in warden_counts/resources/app_data/internal_source/*; do
            echo "Checking WARDEN (counts): $(basename "$subdir")"
            result=$(diff -r -q "$subdir" warden_fastq/resources/app_data/internal_source/"$(basename "$subdir")") || true
            if [[ -n "$result" ]]; then
              echo "$result"
              EXITCODE=1
            fi
          done
          exit $EXITCODE