Refactoring #56

	name: Test Grandeur workflow with salmonella

	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_019710395.3_ASM1971039v3 GCA_001652385.2_ASM165238v2 GCA_013344545.1_ASM1334454v1
	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 Salmonella file
	run: \|
	for file in grandeur/seqsero2/seqsero2_results.txt
	do
	head $file
	wc -l $file
	done

Provide feedback