Update mitohifi.py #50
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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' | |