Varscan2/tasks/processSomatic.wdl

task processSomatic {
    
    String sample
    File varscan_snp
    File varscan_indel
    
    String docker
    String cluster_config
    String disk_size

    command <<<
        cp ${varscan_snp} ./
        cp ${varscan_indel} ./
        java -Xmx12g -jar /opt/VarScan.v2.4.3.jar processSomatic ${sample}.VarScan.TN.SNP.vcf
        java -Xmx12g -jar /opt/VarScan.v2.4.3.jar processSomatic ${sample}.VarScan.TN.INDEL.vcf

    >>>

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

    output {
        File varscan_snp_somatic = "${sample}.VarScan.TN.SNP.Somatic.vcf"
        File varscan_snp_germline = "${sample}.VarScan.TN.SNP.Germline.vcf"
        File varscan_snp_loh = "${sample}.VarScan.TN.SNP.LOH.vcf"
        File varscan_snp_somatic_hc = "${sample}.VarScan.TN.SNP.Somatic.hc.vcf"
        File varscan_snp_germline_hc = "${sample}.VarScan.TN.SNP.Germline.hc.vcf"
        File varscan_snp_loh_hc = "${sample}.VarScan.TN.SNP.LOH.hc.vcf"
        File varscan_indel_somatic = "${sample}.VarScan.TN.INDEL.Somatic.vcf"
        File varscan_indel_germline = "${sample}.VarScan.TN.INDEL.Germline.vcf"
        File varscan_indel_loh = "${sample}.VarScan.TN.INDEL.LOH.vcf"
        File varscan_indel_somatic_hc = "${sample}.VarScan.TN.INDEL.Somatic.hc.vcf"
        File varscan_indel_germline_hc = "${sample}.VarScan.TN.INDEL.Germline.hc.vcf"
        File varscan_indel_loh_hc = "${sample}.VarScan.TN.INDEL.LOH.hc.vcf"
    }
}