Delly_pipeline/tasks/delly.wdl

task delly{
    String sample
    File ref_dir
    String fasta
    File sample_tsv
    File tumor_bam
    File tumor_bam_index
    File normal_bam
    File normal_bam_index
    String docker
    String cluster_config
    String disk_size

    command<<<
    /home/delly call -o ${sample}_delly.bcf \
    -g ${ref_dir}/${fasta} \
    ${tumor_bam} ${normal_bam}

    /home/delly filter -p -f somatic \
    -o ${sample}_delly.somatic.bcf -s ${sample_tsv} ${sample}_delly.bcf

    bcftools convert -O v -o ${sample}_delly.somatic.vcf ${sample}_delly.somatic.bcf

    vcftools --vcf ${sample}_delly.somatic.vcf \
    --out ${sample}_delly.somatic.PASS \
    --recode --recode-INFO-all --remove-filtered-all
    >>>

    runtime{
        docker:docker
        cluster:cluster_config
        systemDisk:"cloud_ssd 40"
        dataDisk:"cloud_ssd " + disk_size + " /cromwell_root/"
        timeout:259200
    }

    output{
        File somatic_bcf = "${sample}_delly.somatic.bcf"
        File somatic_vcf = "${sample}_delly.somatic.vcf"
        File pass_vcf = "${sample}_delly.somatic.PASS.recode.vcf"
    }

}