update amrfinder to version 3.11.18-2023-08-08.2 #46

	name: Test Grandeur workflow

	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 reads
	# lecleria genome - not an actual use-case
	wget -q ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR283/002/SRR2838702/SRR2838702_1.fastq.gz
	wget -q ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR283/002/SRR2838702/SRR2838702_2.fastq.gz
	mv *fastq.gz reads/.
	nextflow run . -profile docker --maxcpus 2 --medcpus 2
	cat grandeur/grandeur_summary.tsv

	- name: Check summary files
	run: \|
	for file in grandeur/mlst/mlst_summary.tsv
	do
	head $file
	wc -l $file
	done

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