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71 lines
2.7 KiB
Text
71 lines
2.7 KiB
Text
// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName } from './functions'
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// TODO nf-core: A module file SHOULD only define input and output files as command-line parameters.
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// All other parameters MUST be provided as a string i.e. "options.args"
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// where "params.options" is a Groovy Map that MUST be provided via the addParams section of the including workflow.
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// Any parameters that need to be evaluated in the context of a particular sample
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// e.g. single-end/paired-end data MUST also be defined and evaluated appropriately.
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// TODO nf-core: Software that can be piped together SHOULD be added to separate module files
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// unless there is a run-time, storage advantage in implementing in this way
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// e.g. bwa mem | samtools view -B -T ref.fasta to output BAM instead of SAM.
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// TODO nf-core: Optional inputs are not currently supported by Nextflow. However, "fake files" MAY be used to work around this issue.
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params.options = [:]
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def options = initOptions(params.options)
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process SEQKIT_SPLIT2 {
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tag "$meta.id"
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label 'process_medium'
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publishDir "${params.outdir}",
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
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conda (params.enable_conda ? "bioconda::seqkit=0.15.0" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/seqkit:0.15.0--0"
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} else {
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container "quay.io/biocontainers/seqkit:0.15.0--0"
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}
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input:
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tuple val(meta), path(reads)
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output:
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tuple val(meta), path("*.split/*.fastq.gz"), emit: reads
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path("*.version.txt") , emit: version
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script:
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def software = getSoftwareName(task.process)
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//TODO not sure if this is useful here, as the splits need to be named individually, and this would make the prefix the same and the outputname I am afraid.
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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if(meta.single_end){
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"""
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seqkit \
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split2 \
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$options.args \
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--threads $task.cpus \
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-1 ${reads} \
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--out-dir ${prefix}.split
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echo \$(seqkit --version 2>&1) | sed 's/^.*seqkit //; s/Using.*\$//' > ${software}.version.txt
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"""
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} else {
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"""
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seqkit \
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split2 \
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$options.args \
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--threads $task.cpus \
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-1 ${reads[0]} \
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-2 ${reads[1]} \
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--out-dir ${prefix}.split
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echo \$(seqkit --version 2>&1) | sed 's/^.*seqkit //; s/Using.*\$//' > ${software}.version.txt
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"""
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}
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}
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