nf-core_modules/modules/gatk/realignertargetcreator/main.nf

// TODO nf-core: If in doubt look at other nf-core/modules to see how we are doing things! :)
//               https://github.com/nf-core/modules/tree/master/modules
//               You can also ask for help via your pull request or on the #modules channel on the nf-core Slack workspace:
//               https://nf-co.re/join
// TODO nf-core: A module file SHOULD only define input and output files as command-line parameters.
//               All other parameters MUST be provided using the "task.ext" directive, see here:
//               https://www.nextflow.io/docs/latest/process.html#ext
//               where "task.ext" is a string.
//               Any parameters that need to be evaluated in the context of a particular sample
//               e.g. single-end/paired-end data MUST also be defined and evaluated appropriately.
// TODO nf-core: Software that can be piped together SHOULD be added to separate module files
//               unless there is a run-time, storage advantage in implementing in this way
//               e.g. it's ok to have a single module for bwa to output BAM instead of SAM:
//                 bwa mem | samtools view -B -T ref.fasta
// TODO nf-core: Optional inputs are not currently supported by Nextflow. However, using an empty
//               list (`[]`) instead of a file can be used to work around this issue.

process GATK_REALIGNERTARGETCREATOR {
    tag "$meta.id"
    label 'process_low'

    // TODO nf-core: List required Conda package(s).
    //               Software MUST be pinned to channel (i.e. "bioconda"), version (i.e. "1.10").
    //               For Conda, the build (i.e. "h9402c20_2") must be EXCLUDED to support installation on different operating systems.
    // TODO nf-core: See section in main README for further information regarding finding and adding container addresses to the section below.
    conda (params.enable_conda ? "bioconda::gatk=3.8" : null)
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
        'https://depot.galaxyproject.org/singularity/gatk:3.8--hdfd78af_11':
        'quay.io/biocontainers/gatk:3.8--hdfd78af_11' }"

    input:
    // TODO nf-core: Where applicable all sample-specific information e.g. "id", "single_end", "read_group"
    //               MUST be provided as an input via a Groovy Map called "meta".
    //               This information may not be required in some instances e.g. indexing reference genome files:
    //               https://github.com/nf-core/modules/blob/master/modules/bwa/index/main.nf
    // TODO nf-core: Where applicable please provide/convert compressed files as input/output
    //               e.g. "*.fastq.gz" and NOT "*.fastq", "*.bam" and NOT "*.sam" etc.
    tuple val(meta), path(bam)

    output:
    // TODO nf-core: Named file extensions MUST be emitted for ALL output channels
    tuple val(meta), path("*.bam"), emit: bam
    // TODO nf-core: List additional required output channels/values here
    path "versions.yml"           , emit: versions

    when:
    task.ext.when == null || task.ext.when

    script:
    def args = task.ext.args ?: ''
    def prefix = task.ext.prefix ?: "${meta.id}"
    // TODO nf-core: Where possible, a command MUST be provided to obtain the version number of the software e.g. 1.10
    //               If the software is unable to output a version number on the command-line then it can be manually specified
    //               e.g. https://github.com/nf-core/modules/blob/master/modules/homer/annotatepeaks/main.nf
    //               Each software used MUST provide the software name and version number in the YAML version file (versions.yml)
    // TODO nf-core: It MUST be possible to pass additional parameters to the tool as a command-line string via the "task.ext.args" directive
    // TODO nf-core: If the tool supports multi-threading then you MUST provide the appropriate parameter
    //               using the Nextflow "task" variable e.g. "--threads $task.cpus"
    // TODO nf-core: Please replace the example samtools command below with your module's command
    // TODO nf-core: Please indent the command appropriately (4 spaces!!) to help with readability ;)
    """
    samtools \\
        sort \\
        $args \\
        -@ $task.cpus \\
        -o ${prefix}.bam \\
        -T $prefix \\
        $bam

    cat <<-END_VERSIONS > versions.yml
    "${task.process}":
        gatk: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' ))
    END_VERSIONS
    """
}