NCG-coverage/tasks/BAMReadCount.wdl

task BAMReadCount {

	String sample_id
	File ref_dir
	String fa
	File fai
	File bed
	File bam
	File bai
	String docker
	String cluster_config
	String disk_size

	command <<<
		bam-readcount -w 0 -q1 -f ${ref_dir}/${fa} -l ${bed} ${bam} > ${sample_id}.readcount
	>>>

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

	output {
		File BAMReadCount = "${sample_id}.readcount"
	}
}