Manta_pipeline/workflow.wdl

import "./tasks/manta.wdl" as manta_calling
import "./tasks/AnnotSV.wdl" as AnnotSV


workflow {{ project_name }} {
    File tumor_bam
    File tumor_bam_bai
    File normal_bam
    File normal_bam_bai
    String ref_fasta
    String ref_bed
    File ref_fasta_dir
    String sample_id
    File annotsv_database
    
    # excute env
    String docker_manta
    String cluster_config
    String disk_size
    String docker_annotsv

	call manta_calling.manta_calling as manta_calling_SV{
		input:
			tumor_bam = tumor_bam,
			tumor_bam_bai = tumor_bam_bai,
			normal_bam = normal_bam,
			normal_bam_bai = normal_bam_bai,
			ref_fasta = ref_fasta,
			ref_dir = ref_fasta_dir,
            ref_bed = ref_bed,
			sample_id = sample_id,
			docker = docker_manta,
			cluster_config = cluster_config,
			disk_size = disk_size

	}

#	call AnnotSV.AnnotSV as manta_AnnotSV{
	#	input:
     #           sample=sample_id,
      #          somatic_vcf= manta_calling_SV.somatic_vcf,
       #         germline_vcf = manta_calling_SV.germline_vcf,
        #        annotsv_database=annotsv_database,
         #       docker=docker_annotsv,
          #      cluster_config=cluster_config,
           #     disk_size=disk_size
		#
	#}




}