CNVkit_Sequenza/workflow.wdl

import "./tasks/CNVkit.wdl" as cnvkit
import "./tasks/AnnotSV.wdl" as AnnotSV
import "./tasks/HRD.wdl" as HRD

workflow {{ project_name }} {
    String sample_id
    File ref_fasta_dir
    String ref_fasta
    File ref_flat
    File gc
    File tumor_bam
    File tumor_bam_bai
    File? normal_bam
    File? normal_bam_bai
    String docker_cnvkit
    String cluster_config
    String disk_size
    File annotsv_database
    String docker_annotsv
    String docker_sequenza

    call HRD.HRD as HRD{
        input:
            sample=sample_id,
            fasta=ref_fasta,
            ref_dir=ref_fasta_dir,
            gc=gc,
            normal_bam=normal_bam,
            normal_bam_index=normal_bam_bai,
            tumor_bam=tumor_bam,
            tumor_bam_index=tumor_bam_bai,
            docker=docker_sequenza,
            cluster_config=cluster_config,
            disk_size=disk_size
    }


    call cnvkit.cnvkit as cnvkit{
        input:
            sample_id=sample_id,
            ref_dir=ref_fasta_dir,
            fasta=ref_fasta,
            ref_flat=ref_flat,
            hrd=HRD.hrd,
            tumor_bam=tumor_bam,
            tumor_bam_index=tumor_bam_bai,
            normal_bam=normal_bam,
            normal_bam_index=normal_bam_bai,
            docker=docker_cnvkit,
            cluster_config=cluster_config,
            disk_size=disk_size
    }

	call AnnotSV.AnnotSV as cnvkit_AnnotSV{
		input:
                sample=sample_id,
                somatic_vcf=cnvkit.cnv_bed,
                annotsv_database=annotsv_database,
                docker=docker_annotsv,
                cluster_config=cluster_config,
                disk_size=disk_size
		
}


}