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
    File ref_fasta_dir
    String sample_id
    File annotsv_database
    
    # excute env
    String docker_manta
    String cluster_config
    String disk_size
    String docker_bcftools
    String docker_annotsv

	call manta_calling.manta_calling as manta_calling{
		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,
			sample_id = sample_id,
			docker = docker_manta,
			cluster_config = cluster_config,
			disk_size = disk_size

	}

	call AnnotSV.AnnotSV as delly_AnnotSV{
		input:
                sample=sample_id,
                somatic_vcf= manta_calling.manta_indel_vcf,
                annotsv_database=annotsv_database,
                docker=docker_annotsv,
                cluster_config=cluster_config,
                disk_size=disk_size
		
	}




}