CNVkit_pipeline/workflow.wdl

import "./tasks/CNVkit.wdl" as cnvkit
import "./tasks/CNVkit_multi_REF.wdl" as cnvkit_multi
import "./tasks/AnnotSV.wdl" as AnnotSV

workflow {{ project_name }} {
    String sample_id
    File ref_fasta_dir
    File ref_fasta_cnvkit
    String ref_fasta
    File ref_flat
    File? bed_file
    String Ploidy
    File gc
    File tumor_bam
    File tumor_bam_bai
    File? normal_bam
    File? normal_bam_bai
    Array[File]? inputBams
    Array[File]? inputBamIndexs
    String docker_cnvkit
    String cluster_config
    String disk_size
    File annotsv_database
    String docker_annotsv
    String docker_sequenza

    if (defined(normal_bams) && size(normal_bams) > 0) {
	    call cnvkit_multi.cnvkit_multi as cnvkit_multi{
            input:
                sample_id=sample_id,
                ref_dir=ref_fasta_cnvkit,
                fasta=ref_fasta,
                ref_flat=ref_flat,
                Ploidy=Ploidy,
                bed_file=bed_file,
                tumor_bam=tumor_bam,
                tumor_bam_index=tumor_bam_bai,
                normal_bams = inputBams,
                normal_bam_indexs = inputBamIndexs,
                docker=docker_cnvkit,
                cluster_config=cluster_config,
                disk_size=disk_size
     }
    }else{
        call cnvkit.cnvkit as cnvkit{
            input:
                sample_id=sample_id,
                ref_dir=ref_fasta_cnvkit,
                fasta=ref_fasta,
                ref_flat=ref_flat,
                Ploidy=Ploidy,
                bed_file=bed_file,
                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
		
   }


}