primers #21

	name: Test SARS-CoV-2 primers

	on: [pull_request, workflow_dispatch]

	run-name: primers

	jobs:

	test:
	runs-on: ubuntu-20.04
	strategy:
	matrix:
	primer: [
	'midnight_idt_V1',
	'midnight_ont_V1',
	'midnight_ont_V2',
	'midnight_ont_V3',
	'ncov_V3',
	'ncov_V4',
	'ncov_V4.1',
	'ncov_V5.3.2',
	'mpx_primalseq'
	]

	steps:
	- name: Checkout
	uses: actions/checkout@v3

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

	- name: Download reads
	run: \|
	mkdir nanopore
	cd nanopore
	wget -q ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR224/050/SRR22452250/SRR22452250_1.fastq.gz
	wget -q ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR224/031/SRR22452231/SRR22452231_1.fastq.gz
	cd ../

	- name: Run Cecret
	run: \|
	nextflow run . -profile docker -c .github/workflows/github_actions.config \
	--maxcpus 2 \
	--medcpus 2 \
	--primer_set ${{ matrix.primer }} \
	--bcftools_variants false \
	--fastqc false \
	--ivar_variants false \
	--samtools_stats false \
	--samtools_coverage false \
	--samtools_depth false \
	--samtools_flagstat false \
	--kraken2 false \
	--nextclade false \
	--pangolin false \
	--freyja false \
	--vadr false \
	--relatedness false \
	--snpdists false \
	--iqtree2 false \
	--bamsnap false \
	--rename false \
	--filter false \
	--multiqc false

	ls cecret*

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

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