samtools-depth/workflow.wdl

import "./tasks/depth.wdl" as depth
import "./tasks/count.wdl" as count

workflow {{ project_name }} {
	File bam
	File bai
	String sample_id
	File bed
	String samtools_docker
	String count_docker
	String cluster_config
	String disk_size

	call depth.depth as depth {
		input:
		bam=bam,
		bai=bai,
		sample_id=sample_id,
		bed=bed,
		docker=samtools_docker,
		cluster_config=cluster_config,
		disk_size=disk_size
	}

    call count.count as count {
        input:
        readcount=depth.bam_depth,
        bed=bed,
        docker=count_docker,
        disk_size=disk_size,
        cluster_config=cluster_config,
        sample_id=sample_id
    }
}