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84cb78cc98
* Templates for new module * pe only test passing * only_pe and only_se passing * only_pe, only_se, mixed passes * Multiple pe + se tc passes * Passing args works * Add 'interleaved' to description * Fixed linting message * Update modules/khmer/normalizebymedian/main.nf Good point. Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com> * Update meta.yml Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
49 lines
1.6 KiB
Text
49 lines
1.6 KiB
Text
// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
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params.options = [:]
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options = initOptions(params.options)
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process KHMER_NORMALIZEBYMEDIAN {
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tag "${name}"
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label 'process_long'
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publishDir "${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), meta:[:], publish_by_meta:[]) }
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conda (params.enable_conda ? "bioconda::khmer=3.0.0a3" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/khmer:3.0.0a3--py37haa7609a_2"
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} else {
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container "quay.io/biocontainers/khmer:3.0.0a3--py37haa7609a_2"
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}
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input:
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path pe_reads
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path se_reads
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val name
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output:
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path "${name}.fastq.gz", emit: reads
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path "versions.yml" , emit: versions
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script:
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pe_args = pe_reads ? "--paired" : ""
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se_args = se_reads ? "--unpaired-reads ${se_reads}" : ""
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files = pe_reads ? pe_reads : se_reads
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"""
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normalize-by-median.py \\
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-M ${task.memory.toGiga()}e9 \\
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--gzip ${options.args} \\
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-o ${name}.fastq.gz \\
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${pe_args} \\
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${se_args} \\
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${files}
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$( normalize-by-median.py --version 2>&1 | grep ^khmer | sed 's/^khmer //' )
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END_VERSIONS
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"""
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}
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