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Update mitohifi.py

Update mitohifi.py #50

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'