Update 20240806 #27

	name: Test Grandeur workflow with sample sheet

	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 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/.

	echo "sample,fastq_1,fastq_2" > sample_sheet.csv
	echo "SRR2838702,reads/SRR2838702_1.fastq.gz,reads/SRR2838702_2.fastq.gz" >> sample_sheet.csv

	nextflow run . -profile docker -c .github/workflows/github_actions.config --sample_sheet sample_sheet.csv --skip_extras

	- name: Check summary files
	run: \|
	for file in grandeur/contigs/*_contigs.fa
	do
	head $file
	wc -l $file
	done

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