parsing contigs_stats #48
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| 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' | |