test #57

	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'

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