rnaseq-engineering/tasks/qualimap.wdl

task qualimap {
	File bam
	File bai
	File gtf
	String bamname = basename(bam, ".sorted.bam")
	String docker
	String cluster
	String disk_size

	command <<<
		set -o pipefail
		set -e
		nt=$(nproc)
		/opt/qualimap/qualimap rnaseq -bam ${bam} -outformat HTML -outdir ${bamname}_rnaseq -gtf ${gtf} -pe --java-mem-size=10G
		/opt/qualimap/qualimap bamqc -bam ${bam} -outformat PDF:HTML -nt $nt -outdir ${bamname}_bamqc --java-mem-size=32G 
		tar -zcf ${bamname}_rnaseq_qualimap.tar.gz ${bamname}_rnaseq
		tar -zcf ${bamname}_bamqc_qualimap.tar.gz ${bamname}_bamqc
	>>>

	runtime {
		docker:docker
		cluster:cluster
		systemDisk:"cloud_ssd 40"
		dataDisk:"cloud_ssd " + disk_size + " /cromwell_root/"
	}

	output {
		File rnaseq_gz = "${bamname}_rnaseq_qualimap.tar.gz"
		File bamqc_gz = "${bamname}_bamqc_qualimap.tar.gz"
	}
}