TNseq/tasks/TNseq_1.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{
        File raw_vcf = "${sample_id}.TNseq.raw.vcf"
        File raw_vcf_index = "${sample_id}.TNseq.raw.vcf.idx"
        File vcf = "${sample_id}.bwa_TNseq.vcf"
        File vcf_index = "${sample_id}.bwa_TNseq.vcf.idx"
        File contamination = "${sample_id}.contamination"
        File contamination_segments = "${sample_id}.contamination.segments"
        File orientation = "${sample_id}.orientation"


    }
}