cnv_common_tasks.wdl

#tag gatk4.0.1.2 release
task PreprocessIntervals {
    File? intervals
    File ref_fasta
    File ref_fasta_fai
    File ref_fasta_dict
    Int? padding
    Int? bin_length
    File? gatk4_jar_override

    # Runtime parameters
    String gatk_docker
    Int? mem_gb
    Int? disk_space_gb
    Boolean use_ssd = false
    Int? cpu
    Int? preemptible_attempts

    Int machine_mem_mb = select_first([mem_gb, 2]) * 1000
    Int command_mem_mb = machine_mem_mb - 500

    # Determine output filename
    String filename = select_first([intervals, "wgs"])
    String base_filename = basename(filename, ".interval_list")

    command <<<
        set -e
        export GATK_LOCAL_JAR=${default="/root/gatk.jar" gatk4_jar_override}

        gatk --java-options "-Xmx${command_mem_mb}m" PreprocessIntervals \
            ${"-L " + intervals} \
            --sequence-dictionary ${ref_fasta_dict} \
            --reference ${ref_fasta} \
            --padding ${default="250" padding} \
            --bin-length ${default="1000" bin_length} \
            --interval-merging-rule OVERLAPPING_ONLY \
            --output ${base_filename}.preprocessed.interval_list
    >>>

    runtime {
        docker: "${gatk_docker}"
        memory: machine_mem_mb + " MB"
        disks: "local-disk " + select_first([disk_space_gb, 40]) + if use_ssd then " SSD" else " HDD"
        cpu: select_first([cpu, 1])
        preemptible: select_first([preemptible_attempts, 5])
    }

    output {
        File preprocessed_intervals = "${base_filename}.preprocessed.interval_list"
    }
}

task AnnotateIntervals {
    File intervals
    File ref_fasta
    File ref_fasta_fai
    File ref_fasta_dict
    File? gatk4_jar_override

    # Runtime parameters
    String gatk_docker
    Int? mem_gb
    Int? disk_space_gb
    Boolean use_ssd = false
    Int? cpu
    Int? preemptible_attempts

    Int machine_mem_mb = select_first([mem_gb, 2]) * 1000
    Int command_mem_mb = machine_mem_mb - 500

    command <<<
        set -e
        export GATK_LOCAL_JAR=${default="/root/gatk.jar" gatk4_jar_override}

        gatk --java-options "-Xmx${command_mem_mb}m" AnnotateIntervals \
            -L ${intervals} \
            --reference ${ref_fasta} \
            --interval-merging-rule OVERLAPPING_ONLY \
            --output annotated_intervals.tsv
    >>>

    runtime {
        docker: "${gatk_docker}"
        memory: machine_mem_mb + " MB"
        disks: "local-disk " + select_first([disk_space_gb, ceil(size(ref_fasta, "GB")) + 50]) + if use_ssd then " SSD" else " HDD"
        cpu: select_first([cpu, 1])
        preemptible: select_first([preemptible_attempts, 5])
    }

    output {
        File annotated_intervals = "annotated_intervals.tsv"
    }
}

task CollectCounts {
    File intervals
    File bam
    File bam_idx
    File ref_fasta
    File ref_fasta_fai
    File ref_fasta_dict
    String? format
    File? gatk4_jar_override

    # Runtime parameters
    String gatk_docker
    Int? mem_gb
    Int? disk_space_gb
    Boolean use_ssd = false
    Int? cpu
    Int? preemptible_attempts

    Int machine_mem_mb = select_first([mem_gb, 7]) * 1000
    Int command_mem_mb = machine_mem_mb - 1000

    # Sample name is derived from the bam filename
    String base_filename = basename(bam, ".bam")
    String counts_filename = if !defined(format) then "${base_filename}.counts.hdf5" else "${base_filename}.counts.tsv"

    command <<<
        set -e
        export GATK_LOCAL_JAR=${default="/root/gatk.jar" gatk4_jar_override}

        gatk --java-options "-Xmx${command_mem_mb}m" CollectFragmentCounts \
            -L ${intervals} \
            --input ${bam} \
            --reference ${ref_fasta} \
            --format ${default="HDF5" format} \
            --interval-merging-rule OVERLAPPING_ONLY \
            --output ${counts_filename}
    >>>

    runtime {
        docker: "${gatk_docker}"
        memory: machine_mem_mb + " MB"
        disks: "local-disk " + select_first([disk_space_gb, ceil(size(bam, "GB")) + 50]) + if use_ssd then " SSD" else " HDD"
        cpu: select_first([cpu, 1])
        preemptible: select_first([preemptible_attempts, 5])
    }

    output {
        String entity_id = base_filename
        File counts = counts_filename
    }
}

task CollectAllelicCounts {
    File common_sites
    File bam
    File bam_idx
    File ref_fasta
    File ref_fasta_fai
    File ref_fasta_dict
    Int? minimum_base_quality
    File? gatk4_jar_override

    # Runtime parameters
    String gatk_docker
    Int? mem_gb
    Int? disk_space_gb
    Boolean use_ssd = false
    Int? cpu
    Int? preemptible_attempts

    Int machine_mem_mb = select_first([mem_gb, 13]) * 1000
    Int command_mem_mb = machine_mem_mb - 1000

    # Sample name is derived from the bam filename
    String base_filename = basename(bam, ".bam")

    String allelic_counts_filename = "${base_filename}.allelicCounts.tsv"

    command <<<
        set -e
        export GATK_LOCAL_JAR=${default="/root/gatk.jar" gatk4_jar_override}

        gatk --java-options "-Xmx${command_mem_mb}m" CollectAllelicCounts \
            -L ${common_sites} \
            --input ${bam} \
            --reference ${ref_fasta} \
            --minimum-base-quality ${default="20" minimum_base_quality} \
            --output ${allelic_counts_filename}
    >>>

    runtime {
        docker: "${gatk_docker}"
        memory: machine_mem_mb + " MB"
        disks: "local-disk " + select_first([disk_space_gb, ceil(size(bam, "GB")) + 50]) + if use_ssd then " SSD" else " HDD"
        cpu: select_first([cpu, 1])
        preemptible: select_first([preemptible_attempts, 5])
    }

    output {
        String entity_id = base_filename
        File allelic_counts = allelic_counts_filename
    }
}

task ScatterIntervals {
    File interval_list
    Int num_intervals_per_scatter

    # Runtime parameters
    String gatk_docker
    Int? mem_gb
    Int? disk_space_gb
    Boolean use_ssd = false
    Int? cpu
    Int? preemptible_attempts

    Int machine_mem_mb = select_first([mem_gb, 2]) * 1000

    String base_filename = basename(interval_list, ".interval_list")

    command <<<
        set -e

        grep @ ${interval_list} > header.txt
        grep -v @ ${interval_list} > all_intervals.txt
        split -l ${num_intervals_per_scatter} --numeric-suffixes all_intervals.txt ${base_filename}.scattered.
        for i in ${base_filename}.scattered.*; do cat header.txt $i > $i.interval_list; done
    >>>

    runtime {
        docker: "${gatk_docker}"
        memory: machine_mem_mb + " MB"
        disks: "local-disk " + select_first([disk_space_gb, 40]) + if use_ssd then " SSD" else " HDD"
        cpu: select_first([cpu, 1])
        preemptible: select_first([preemptible_attempts, 5])
    }

    output {
        Array[File] scattered_interval_lists = glob("${base_filename}.scattered.*.interval_list")
    }
}

task PostprocessGermlineCNVCalls {
    String entity_id
    Array[File] chunk_path_tars
    String sample_index
    File? gatk4_jar_override

    # Runtime parameters
    String gatk_docker
    Int? mem_gb
    Int? disk_space_gb
    Boolean use_ssd = false
    Int? cpu
    Int? preemptible_attempts

    Int machine_mem_mb = select_first([mem_gb, 7]) * 1000
    Int command_mem_mb = machine_mem_mb - 1000

    String sample_directory = "SAMPLE_${sample_index}"  #this is a hardcoded convention in gcnvkernel
    String vcf_filename = "${entity_id}.vcf.gz"

    String dollar = "$" #WDL workaround for using array[@], see https://github.com/broadinstitute/cromwell/issues/1819

    command <<<
        set -e
        export GATK_LOCAL_JAR=${default="/root/gatk.jar" gatk4_jar_override}

        #untar chunk_path_tars to CHUNK_0, CHUNK_1, etc. directories and build chunk_paths_command_line="--chunk_path CHUNK_0 ..."
        chunk_path_array=(${sep=" " chunk_path_tars})
        chunk_paths_command_line=""
        for index in ${dollar}{!chunk_path_array[@]}; do
            chunk_path_tar=${dollar}{chunk_path_array[$index]}
            mkdir CHUNK_$index
            tar xzf $chunk_path_tar -C CHUNK_$index
            chunk_paths_command_line="$chunk_paths_command_line --chunk-path CHUNK_$index"
        done

        gatk --java-options "-Xmx${command_mem_mb}m" PostprocessGermlineCNVCalls \
            $chunk_paths_command_line \
            --sample-directory ${sample_directory} \
            --output ${vcf_filename}
    >>>

    runtime {
        docker: "${gatk_docker}"
        memory: machine_mem_mb + " MB"
        disks: "local-disk " + select_first([disk_space_gb, 40]) + if use_ssd then " SSD" else " HDD"
        cpu: select_first([cpu, 1])
        preemptible: select_first([preemptible_attempts, 5])
    }

    output {
        File vcf = vcf_filename
    }
}