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d5183a7fec
* add cellranger mkref module * add cellranger mkref tests * update test yml chksum * fix module linting * fix test yml * fix getprocessname * fix versions typo * fix cellranger test.yml * fix versions.yml * test versions.yml * fix grep version * fix cellranger version * add dockerfile and readme * review container statement * Update modules/cellranger/mkref/meta.yml Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> * add disclaimers * change location dockerfile Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
40 lines
1.2 KiB
Text
40 lines
1.2 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 CELLRANGER_MKREF {
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tag 'mkref'
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label 'process_high'
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publishDir "${params.outdir}",
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
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if (params.enable_conda) {
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exit 1, "Conda environments cannot be used when using the Cell Ranger tool. Please use docker or singularity containers."
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}
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container "nfcore/cellranger:6.0.2"
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input:
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path fasta
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path gtf
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val(reference_name)
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output:
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path "versions.yml" , emit: versions
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path "${reference_name}", emit: reference
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script:
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"""
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cellranger mkref \\
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--genome=${reference_name} \\
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--fasta=${fasta} \\
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--genes=${gtf}
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(echo \$( cellranger --version 2>&1) | sed 's/^.*[^0-9]\\([0-9]*\\.[0-9]*\\.[0-9]*\\).*\$/\\1/' )
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END_VERSIONS
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"""
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}
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