Manta_pipeline/tasks/manta.wdl

task manta_calling{
    File tumor_bam
    File tumor_bam_bai
    File normal_bam
    File normal_bam_bai
    String ref_fasta
    String ref_bed
    File ref_dir
    String sample_id
    
    String docker
    String cluster_config
    String disk_size

    
    String out_dir = "${sample_id}_result"
    command <<<
    set -exo pipefail
    nt=$(nproc)
    if [ ${normal_bam} ]; then
      INPUT="--normalBam ${normal_bam} --tumorBam ${tumor_bam}"
    else
      INPUT="--tumorBam ${tumor_bam}"
    fi
    /home/biosoft/manta-1.6.0.centos6_x86_64/bin/configManta.py \
    $INPUT \
    --referenceFasta ${ref_dir}/${ref_fasta} \
    --callRegions ${ref_dir}/${ref_bed} \
    --runDir ${out_dir}
    
    ls ${out_dir}

    python2.7 ${out_dir}/runWorkflow.py -m local -j $nt

    ls ${out_dir}

    if [ ${normal_bam} ]; then
      cp ${out_dir}/results/variants/somaticSV.vcf.gz ${sample_id}.Manta.somaticSV.vcf.gz
      cp ${out_dir}/results/variants/diploidSV.vcf.gz ${sample_id}.Manta.germlineSV.vcf.gz
    else
      cp ${out_dir}/results/variants/tumorSV.vcf.gz ${sample_id}.Manta.somaticSV.vcf.gz
    fi
    >>>

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

    }

    output{
    	File somatic_vcf = "${sample_id}.Manta.somaticSV.vcf.gz"
    	File? germline_vcf = "${sample_id}.Manta.germlineSV.vcf.gz"
    }
}