variant-calling/tasks/TNscope.wdl

task TNscope {


    String sample
    String SENTIEON_INSTALL_DIR
    String SENTIEON_LICENSE
    File tumor_recaled_bam
    File tumor_recaled_bam_index
    File tumor_recal_table
    File normal_recaled_bam
    File normal_recaled_bam_index
    File normal_recal_table
    String tumor_name
    String normal_name

    File ref_dir
    String fasta
    File dbsnp_dir
    String dbsnp
    File? regions
    
    String docker
    String cluster_config	
    String disk_size

    Boolean set_pon
    File? pon_vcf
    String pon_command = if set_pon then "--pon /cromwell_root/tmp/PON/$(basename ${pon_vcf})" else ""
    
    command <<<
        set -o pipefail
        set -e
        export SENTIEON_LICENSE=${SENTIEON_LICENSE}
        nt=$(nproc)

        if ${set_pon}; then
            mkdir -p /cromwell_root/tmp/PON/
            cp ${pon_vcf} /cromwell_root/tmp/PON/
            ${SENTIEON_INSTALL_DIR}/bin/sentieon util vcfindex /cromwell_root/tmp/PON/$(basename ${pon_vcf})
        fi
        
        if [ ${regions} != "" ]; then
            ${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt \
            --interval ${regions} -r ${ref_dir}/${fasta} \
            -i ${tumor_recaled_bam} -q ${tumor_recal_table} \
            -i ${normal_recaled_bam} -q ${normal_recal_table} \
            --algo TNscope \
            --tumor_sample ${tumor_name} --normal_sample ${normal_name} \
            --dbsnp ${dbsnp_dir}/${dbsnp} \
            ${pon_command} \
            ${sample}.TNscope.TN.vcf
        else
            ${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt \
            -r ${ref_dir}/${fasta} \
            -i ${tumor_recaled_bam} -q ${tumor_recal_table} \
            -i ${normal_recaled_bam} -q ${normal_recal_table} \
            --algo TNscope \
            --tumor_sample ${tumor_name} --normal_sample ${normal_name} \
            --dbsnp ${dbsnp_dir}/${dbsnp} \
            ${pon_command} \
            ${sample}.TNscope.TN.vcf		
        fi
    >>>

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

    output {
        File TNscope_vcf= "${sample}.TNscope.TN.vcf"
        File TNscope_vcf_index = "${sample}.TNscope.TN.vcf.idx"
    }

}