mergefq/tasks/mergefq.wdl

task mergefq {
	file fq_list
	String fq_m
	String disk_size
	String cluster_config

	command <<<
		set -euo pipefail
		cat ${fq_list}|IFS=";" read -a myarray
        cat ${myarray[@]} >${fq_m}
		
	>>>

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

	output {
		File merge_fq = "${fq_m}"
	}
}