wgs_somatic_pipeline_v1/tasks/manta.wdl

task manta_calling{
    File tumour_bam
    File tumour_bam_bai
    File normal_bam
    File normal_bam_bai
    String ref_fasta
    File ref_dir
    String sample_id
    
    String docker
    String cluster_config
    String disk_size

    
    String out_dir = "${sample_id}_result"
    command <<<
    set -exo pipefail
    /home/biosoft/manta-1.6.0.centos6_x86_64/bin/configManta.py \
    --normalBam ${normal_bam} \
    --tumorBam ${tumour_bam} \
    --referenceFasta ${ref_dir}/${ref_fasta} \
    --runDir ${out_dir}
    
    ls ${out_dir}

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

    ls ${out_dir}

    tar cvf ${out_dir}.tar ${out_dir}
    >>>

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

    }

    output{
        File out_file = "${out_dir}.tar"
        File manta_indel_vcf = "${out_dir}/results/variants/candidateSmallIndels.vcf.gz"
        File manta_indel_vcf_index = "${out_dir}/results/variants/candidateSmallIndels.vcf.gz.tbi"
    }
}