strelka_pipeline/workflow.wdl

import "./tasks/stralka.wdl" as stralka

workflow {{ project_name }} {
    File tumour_bam
    File tumour_bam_bai
    File normal_bam
    File normal_bam_bai
    String ref_fasta
    File ref_dir
    String sample_id
    File? manta_indel_vcf
    File? manta_indel_vcf_index
    
    # excute env
    String docker_stralka
    String cluster_config
    String disk_size

    call stralka.strelka_calling as stralka{
        input:
            tumour_bam=tumour_bam,
            tumour_bam_bai=tumour_bam_bai,
            normal_bam=normal_bam,
            normal_bam_bai=normal_bam_bai,
            ref_fasta=ref_fasta,
            ref_dir=ref_dir,
            sample_id=sample_id,
            docker=docker_stralka,
            cluster_config=cluster_config,
            disk_size=disk_size
    }

}