TNseq/tasks/TNseq_test.wdl

task sentieon_TNseq{
    String sample_id
    File tumor_bam
    File tumor_bam_bai
    File? normal_bam
    File? normal_bam_bai
    String tumor_name
    String normal_name

    File ref_dir
    String ref_fasta
    File germline_resource
    File germline_resource_tbi
    File? regions
    Int? interval_padding

    # excute env
    String docker
    String cluster_config
    String disk_size
    String SENTIEON_LICENSE


    command <<<
        set -o pipefail
        set -exo
        export SENTIEON_LICENSE=${SENTIEON_LICENSE}
        nt=$(nproc)
        
        sentieon licclnt ping -s 172.25.2.5:8990 && echo 'It works.'


    >>>

    runtime{
        docker:docker
        cluster:cluster_config
        systemDisk:"cloud_ssd 40"
        dataDisk:"cloud_ssd " + disk_size + " /cromwell_root/"

    }

    output{

    }
}