github-actions-integration-test.yml

name: MitoHiFi Integration Test

on:  # workflow_dispatch
  push:
    branches:
    - 'master'
  
jobs:
  integration_test:
    runs-on: ubuntu-latest
    steps:
      - name: Checkout code
        uses: actions/checkout@v2
      
      
      - name: Run integration test_contigs with Docker
        run: |
          docker run --name test_contigs \
          ghcr.io/marcelauliano/mitohifi:master \
            mitohifi.py \
            -c /opt/MitoHiFi/tests/ilPhaBuce1_contig.fa \
            -f /opt/MitoHiFi/tests/NC_016067.1.fasta \
            -g /opt/MitoHiFi/tests/NC_016067.1.gb \
            -o 5 \
            -t 1
      - name: compare_contigs
        run: |
          docker cp test_contigs:/tmp/final_mitogenome.gb ./
          cmp tests/ilPhaBuce1_final_mitogenome.gb final_mitogenome.gb && echo 'SUCCESS CONTIGS'
      
      - name: Run integration test_reads with Docker
        run: |
          docker run --name test_reads \
          ghcr.io/marcelauliano/mitohifi:master \
            mitohifi.py \
            -r /opt/MitoHiFi/tests/ilDeiPorc1.reads.100.fa \
            -f /opt/MitoHiFi/tests/MW539688.1.fasta \
            -g /opt/MitoHiFi/tests/MW539688.1.gb \
            --mitos \
            -o 5 \
            -t 1
      - name: compare_reads
        run: |
          docker cp test_reads:/tmp/final_mitogenome.fasta ./
          cmp tests/ilDeiPorc1.final_mitogenome.fasta final_mitogenome.fasta && echo 'SUCCESS READS & MITOS'