TNscope/workflow.wdl

import "./tasks/TNscope.wdl" as TNscope

workflow {{ project_name }} {
    String sample_id
    File tumor_bam
    File tumor_bam_bai
    File? normal_bam
    File? normal_bam_bai
    String tumor_name
    String normal_name
    File tumor_recall_data
    File normal_recall_data

    File ref_dir
    String ref_fasta
    File dbsnp_dir
    String dbsnp

    # excute env
    String docker_sentieon
    String cluster_config
    String disk_size
    String SENTIEON_LICENSE

    call TNscope.sentieon_TNscope as sentieon_TNscope{
        input:
            sample_id=sample_id,
            tumor_bam=tumor_bam,
            tumor_bam_bai=tumor_bam_bai,
            normal_bam=normal_bam,
            normal_bam_bai=normal_bam_bai,
            tumor_name=sample_id+'_T',
            normal_name=sample_id+'_N',
            tumor_recall_data=tumor_recall_data,
            normal_recall_data=normal_recall_data,
            ref_dir=ref_dir,
            ref_fasta=ref_fasta,
            dbsnp_dir=dbsnp_dir,
            dbsnp=dbsnp,
            docker=docker_sentieon,
            cluster_config=cluster_config,
            disk_size=disk_size,
            SENTIEON_LICENSE=SENTIEON_LICENSE


    }


}