Download fastq and fasta and run #168

	name: Test SARS-CoV-2 workflow

	on: [pull_request, workflow_dispatch]

	run-name: Download fastq and fasta and run

	jobs:

	test:
	runs-on: ubuntu-20.04
	steps:
	- name: Checkout
	uses: actions/checkout@master
	with:
	lfs: true

	- name: Checkout LFS objects
	run: git lfs checkout

	- name: Install Nextflow
	run: \|
	wget -qO- get.nextflow.io \| bash
	sudo mv nextflow /usr/local/bin/

	- name: Run Cecret
	run: \|
	docker --version

	mkdir reads
	wget -q ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR139/023/SRR13957123/SRR13957123_1.fastq.gz
	wget -q ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR139/023/SRR13957123/SRR13957123_2.fastq.gz
	mv *fastq.gz reads/.

	mkdir -p fastas
	wget -q https://raw.githubusercontent.com/StaPH-B/docker-builds/master/tests/SARS-CoV-2/SRR13957123.consensus.fa
	mv SRR13957123.consensus.fa SRR13957123DB.fa
	mv *fa fastas/.

	nextflow run . -profile docker -c .github/workflows/github_actions.config --primer_set ncov_V3 --maxcpus 2 --medcpus 2 --cleaner 'fastp' --aligner 'minimap2' --mpileup_depth 200

	ls cecret*

	cat cecret*/cecret_results.txt

	- name: Clean
	run: rm -rf work .nextflow*

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