variant-calling/tasks/somatic.wdl

task somatic {

    String sample
    File normal_bam
    File normal_bam_index
    File tumor_bam
    File tumor_bam_index

    File ref_dir
    String fasta    
    String docker
    String cluster_config
    String disk_size

    command <<<
        samtools mpileup -f ${ref_dir}/${fasta} -B ${normal_bam} ${tumor_bam} | java -Xmx12g -jar /opt/VarScan.v2.4.3.jar somatic --mpileup 1 --min-coverage 3 --min-coverage-normal 3 --min-coverage-tumor 3 --min-var-freq 0.08 --p-value 0.10 --somatic-p-value 0.05 --output-vcf 1 --output-snp ${sample}.VarScan.TN.SNP --output-indel ${sample}.VarScan.TN.INDEL --strand-filter 1
    >>>

    runtime {
        docker: docker
        cluster: cluster_config
        systemDisk: "cloud_ssd 40"
        dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
    }
    output {
        File varscan_snp = "${sample}.VarScan.TN.SNP.vcf"
        File varscan_indel = "${sample}.VarScan.TN.INDEL.vcf"
        
    }
}