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

workflow {{ project_name }} {
	#sample info
    File? normal_in1
    File? normal_in2
	File? tumor_in1
	File? tumor_in2
    String sample_id
	String Seq_platform
	#reference fasta
	String ref_fasta
	File ref_fasta_dir
	File annot_gff
    File dbsnp_dir
    File dbmills_dir
    String dbsnp
    String db_mills
    File? regions
    Int? interval_padding
	File germline_resource
	File germline_resource_tbi

	#docker
    String docker_fastp
	String docker_sentieon
	String SENTIEON_LICENSE
	String docker_qualimap
	String docker_manta
	String docker_strelka

	#config
    String cluster_config
    String disk_size
	Boolean? fastqc
	Boolean bamqc


	call TNseq.sentieon_TNseq as sentieon_TNseq{
	input:
		sample_id = sample_id,
		tumor_bam = Sentieon_BQSR_tumor.recaled_bam,
		tumor_bam_bai = Sentieon_BQSR_tumor.recaled_bam_index,
		normal_bam = Sentieon_BQSR_normal.recaled_bam,
		normal_bam_bai = Sentieon_BQSR_normal.recaled_bam_index,
		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
}

}