ASCAT_pipeline/workflow.wdl

version 1.0
import "./tasks/ASCAT.wdl" as ascat

workflow {{ project_name }} {
    String sample
    File tumor_bam
    File tumor_bam_index
    File? normal_bam
    File? normal_bam_index
    String gender
    String ref_genome
    String docker_ascat
    String cluster_config
    String disk_size

    call cnvkit.cnvkit as cnvkit{
        input:
            sample=sample_id,
            tumor_bam=tumor_bam,
            tumor_bam_index=tumor_bam_bai,
            normal_bam=normal_bam,
            normal_bam_index=normal_bam_bai,
            gender=gender,
            ref_genome=ref_genome,
            docker=docker_ascat,
            cluster_config=cluster_config,
            disk_size=disk_size
    }


}