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
    File? VCF
    String docker_cnvkit
    String cluster_config
    String disk_size
    File annotsv_database
    String docker_annotsv
    String docker_sequenza
    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,
            VCF = VCF,
            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
    
}





}