bwa-mem2.wdl

version 1.0

# Copyright (c) 2017 Leiden University Medical Center
#
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# furnished to do so, subject to the following conditions:
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# The above copyright notice and this permission notice shall be included in
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#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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# SOFTWARE.

task Mem {
    input {
        File read1
        File? read2
        BwaIndex bwaIndex
        String outputPrefix
        Boolean sixtyFour = false
        Boolean usePostalt = false
        Int sortMemoryPerThreadGb = 2
        Int compressionLevel = 1

        String? readgroup
        Int? sortThreads
        
        Int threads = 4
        Int? memoryGb
        Int timeMinutes = 1 + ceil(size([read1, read2], "GiB") * 220 / threads)
        # Contains bwa-mem2 2.0 bwakit 0.7.17.dev1 and samtools 1.10.
        String dockerImage = "quay.io/biocontainers/mulled-v2-6a15c99309c82b345497d24489bee67bbb76c2f6:1c9c3227b9bf825a8dc9726a25701aa23c0b1f12-0"
    }

    # Samtools sort may block the pipe while it is writing data to disk.
    # This can lead to cpu underutilization.
    # 1 thread if threads is 1. For 2-4 threads 2 sort threads. 3 sort threads for 5-8 threads.
    Int estimatedSortThreads = if threads == 1 then 1 else 1 + ceil(threads / 4.0)
    Int totalSortThreads = select_first([sortThreads, estimatedSortThreads])
    # BWA-mem2's index files contain 2 BWT indexes of which only one is used. .2bit64 is used by default and
    # .8bit32 is used for avx2.
    # The larger one of these is the 8bit32 index. Since we do not know beforehand which one is used we need to accomodate for that.
    # Using only the 8bit32 index uses 57,5% of the index files. Since bwa-mem2 uses slightly more memory than the index.
    # We put it at 62% as a safety factor. That means the memory usage for bwa-mem will be 53G for a human genome. Resulting in 60G total
    # on 8 cores with samtools with 3 sort threads.
    Int estimatedMemoryGb = 1 + ceil(size(bwaIndex.indexFiles, "G") * 0.62) + sortMemoryPerThreadGb * totalSortThreads
    
    # The bwa postalt script is out commented as soon as usePostalt = false.
    # This hack was tested with bash, dash and ash. It seems that comments in between pipes work for all of them.
    command {
        set -e
        mkdir -p "$(dirname ~{outputPrefix})"
        bwa-mem2 mem \
          -t ~{threads} \
          ~{"-R '" + readgroup}~{true="'" false="" defined(readgroup)} \
          ~{bwaIndex.fastaFile} \
          ~{read1} \
          ~{read2} \
          2> ~{outputPrefix}.log.bwamem | \
          ~{true="" false="#" usePostalt} bwa-postalt.js -p ~{outputPrefix}.hla ~{bwaIndex.fastaFile}~{true=".64.alt" false=".alt" sixtyFour} | \
          samtools sort \
          ~{"-@ " + totalSortThreads} \
          -m ~{sortMemoryPerThreadGb}G \
          -l ~{compressionLevel} \
          - \
          -o ~{outputPrefix}.aln.bam
    }

    output {
        File outputBam = outputPrefix + ".aln.bam"
        File? outputHla = outputPrefix + ".hla"
    }

    runtime {
        # One extra thread for bwa-postalt + samtools is not needed.
        # These only use 5-10% of compute power and not always simultaneously.
        cpu: threads
        memory: "~{select_first([memoryGb, estimatedMemoryGb])}GiB"
        time_minutes: timeMinutes
        docker: dockerImage
    }

    parameter_meta {
        # inputs
        read1: {description: "The first-end fastq file.", category: "required"}
        read2: {description: "The second-end fastq file.", category: "common"}
        bwaIndex: {description: "The BWA index, including (optionally) a .alt file.", category: "required"}
        outputPrefix: {description: "The prefix of the output files, including any parent directories.", category: "required"}
        sixtyFour: {description: "Whether or not the index uses the '.64' suffixes.", category: "common"}
        usePostalt: {description: "Whether to use the postalt script from bwa kit."}
        sortMemoryPerThreadGb: {description: "The amount of memory for each sorting thread in gigabytes.", category: "advanced"}
        compressionLevel: {description: "The compression level of the output BAM.", category: "advanced"}
        readgroup: {description: "A readgroup identifier.", category: "common"}
        sortThreads: {description: "The number of threads to use for sorting.", category: "advanced"}
        threads: {description: "The number of threads to use for alignment.", category: "advanced"}
        memoryGb: {description: "The amount of memory this job will use in gigabytes.", category: "advanced"}
        timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
        dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}

        # outputs
        outputBam: {description: "The produced BAM file."}
        outputHla: {description: "The produced HLA file."}
    }
}

struct BwaIndex {
    File fastaFile
    Array[File] indexFiles
}