rule run_fastqc:
	input:
		fq1 = lambda wildcards: get_read_files( wildcards.ID )['read1'],
		fq2 = lambda wildcards: get_read_files( wildcards.ID )['read2']
	output:
		html1 = "results/qc/{ID}_1_fastqc.html",
		zip1 = "results/qc/{ID}_1_fastqc.zip",
		html2 = "results/qc/{ID}_2_fastqc.html",
		zip2 = "results/qc/{ID}_2_fastqc.zip"
	params:
		outputdir = "results/qc/"
	shell: """
		fastqc -q -o {params.outputdir} {input.fq1} {input.fq2}
	"""

rule run_multiqc:
	input:
		fastqc_output = expand( 'results/qc/{ID}_{read}_fastqc.zip', ID = [ sample['ID'] for sample in config['samples'] ], read = [ "1", "2" ] )
	output:
		files = temp( "results/qc/tmp/fastqc_file_list.txt" ),
		htmlreport = "results/qc/fastq_multiqc_report.html"
	params:
		outputdir = "results/qc",
		title = "fastq"
	shell: """
		# make a list of files.
		echo {input} | tr " " "\n" > {output.files}
		multiqc -f -z -i {params.title} -o {params.outputdir} --file-list {output.files}
	"""