CNVkit/workflow.wdl

import "./tasks/access.wdl" as access
import "./tasks/batch.wdl" as batch
import "./tasks/export.wdl" as export

workflow {{ project_name }} {	
    String sample_id
    File tumor_bam
    File tumor_bai
    File normal_bam
    File normal_bai
    String bed
    File ref_dir
    String fasta
	String docker
    String cluster
    String disk_size

	call access.access as access {
		input: 
		fasta=fasta,
		ref_dir=ref_dir,
		docker = docker,
		cluster = cluster,
		disk_size = disk_size
	}

	call batch.batch as batch {
		input: 
		sample_id = sample_id,
		fasta=fasta,
		ref_dir=ref_dir,
		tumor_bam = tumor_bam,
		tumor_bai = tumor_bai,
		normal_bam = normal_bam,
		normal_bai = normal_bai,
		bed = bed,
		access_bed = access.access_bed,
		docker = docker,
		cluster = cluster,
		disk_size = disk_size
	}

	call export.export as export {
		input:
		result = batch.result,
		docker = docker,
		cluster = cluster,
		disk_size = disk_size
	}
}