rnaseq-engineering/tasks/fastqscreen.wdl

task fastqscreen {
	File read1
	File read2
	File screen_ref_dir
	File fastq_screen_conf
	String read1name=sub(basename(read1),"\\.\\S+$", "")
	String read2name=sub(basename(read2),"\\.\\S+$", "")
	String docker
	String cluster
	String disk_size

	command <<<
		set -o pipefail
		set -e
		nt=$(nproc)
		mkdir -p /cromwell_root/tmp
		cp -r ${screen_ref_dir} /cromwell_root/tmp/
		# sed -i "s#/cromwell_root/fastq_screen_reference#${screen_ref_dir}#g" ${fastq_screen_conf}
		fastq_screen --aligner bowtie2 --conf ${fastq_screen_conf} --top 100000 --threads $nt ${read1}
		fastq_screen --aligner bowtie2 --conf ${fastq_screen_conf} --top 100000 --threads $nt ${read2}
	>>>

	runtime {
		docker:docker
		cluster: cluster
		systemDisk: "cloud_ssd 40"
		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
	}
	output {
		File png1="${read1name}_screen.png"
		File txt1="${read1name}_screen.txt"
		File html1="${read1name}_screen.html"
		File png2="${read2name}_screen.png"
		File txt2="${read2name}_screen.txt"
		File html2="${read2name}_screen.html"
	}
}