Update 2023 09 20 #34

	name: Test Grandeur workflow with Group A Strep

	on: [pull_request, workflow_dispatch]

	jobs:

	test:
	runs-on: ubuntu-20.04
	steps:
	- name: Checkout
	uses: actions/checkout@v3
	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 Grandeur
	run: \|
	docker --version

	mkdir fastas
	for accession in GCA_001412635.1_ASM141263v1 GCA_016724885.1_ASM1672488v1 GCA_900475035.1_41965_F01
	do
	all=$(echo $accession \| cut -f 2 -d "_")
	fir=$(echo $all \| cut -c 1-3)
	mid=$(echo $all \| cut -c 4-6)
	end=$(echo $all \| cut -c 7-9)
	wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/${fir}/${mid}/${end}/${accession}/${accession}_genomic.fna.gz
	gzip -d ${accession}_genomic.fna.gz
	mv ${accession}_genomic.fna fastas/.
	done

	nextflow run . -profile docker --maxcpus 2 --medcpus 2
	cat grandeur/grandeur_summary.tsv

	- name: Check Strep pneumo file
	run: \|
	for file in grandeur/emmtyper/emmtyper_summary.tsv
	do
	head $file
	wc -l $file
	done

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