TNseq/workflow.wdl

import "./tasks/TNseq.wdl" as TNseq

workflow {{ project_name }} {
	String sample_id
	File tumor_bam
	File tumor_bam_bai
	File normal_bam
	File normal_bam_bai

	File ref_fasta_dir
	String ref_fasta
	File germline_resource
	File germline_resource_tbi

	String docker_sentieon
	String cluster_config
	String disk_size
	String SENTIEON_LICENSE

	call TNseq.sentieon_TNseq as sentieon_TNseq{
	input:
		sample_id = sample_id,
		tumor_bam = tumor_bam,
		tumor_bam_bai = tumor_bam_bai,
		normal_bam = normal_bam,
		normal_bam_bai = normal_bam_bai,
		tumor_name = sample_id+'_T',
		normal_name = sample_id+'_N',

		ref_dir = ref_fasta_dir,
		ref_fasta = ref_fasta,
		germline_resource = germline_resource,
		germline_resource_tbi = germline_resource_tbi,

		docker = docker_sentieon,
		cluster_config = cluster_config,
		disk_size = disk_size,
		SENTIEON_LICENSE = SENTIEON_LICENSE
}

}