per-base-depth/tasks/depth.wdl

task depth {
	File raw_bam
	File raw_bam_idx
	File deduped_bam
	File deduped_bam_idx
	String sample_id
	File regions
	String docker
	String cluster_config
	String disk_size
	
	command <<<
		/opt/conda/bin/samtools depth -aa -b ${regions} ${raw_bam} > ${sample_id}.raw.depth
		/opt/conda/bin/samtools depth -aa -b ${regions} ${deduped_bam} > ${sample_id}.deduped.depth
		sort -k1,1V -k2,2n ${sample_id}.raw.depth | awk '{printf "%s:%i\t%i\n" , $1,$2,$3}' > ${sample_id}.raw.sorted.depth
		sort -k1,1V -k2,2n ${sample_id}.deduped.depth | awk '{printf "%s:%i\t%i\n" , $1,$2,$3}' > ${sample_id}.deduped.sorted.depth
		join -e NULL -a1 -j 1 -o 1.1,1.2,2.2 ${sample_id}.raw.sorted.depth ${sample_id}.deduped.sorted.depth > ${sample_id}.depth
	>>>

	runtime {
		docker:docker
		cluster: cluster_config
		systemDisk: "cloud_ssd 40"
		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
	}
	output {
		File bam_depth = "${sample_id}.depth"
	}
}