Update20240626 #84

	name: Test Grandeur workflow with vibrio

	on: [pull_request, workflow_dispatch]

	jobs:

	test:
	runs-on: ubuntu-20.04
	steps:
	- name: Checkout
	uses: actions/checkout@v4

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

	nextflow -version

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

	mkdir fastas
	for accession in GCA_009665515.2_ASM966551v2 GCA_009763645.1_ASM976364v1 GCA_004355205.1_ASM435520v1 GCA_009665315.1_ASM966531v1 GCA_002953375.1_ASM295337v1
	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 -c .github/workflows/github_actions.config --fastas fastas
	cat grandeur/grandeur_summary.tsv
	cat grandeur/summary/software_versions.yml
	ls grandeur/multiqc/multiqc_report.html

	- name: Check Vibrio species
	run: \|
	grep -i vibrio grandeur/fastani/fastani_summary.csv
	for file in grandeur/kaptive/kaptive_summary.txt
	do
	head $file
	wc -l $file
	done

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