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https://github.com/MillironX/nf-core_modules.git
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1b24005f07
* refactor: add bcl2fastq to cellranger dockerfile bcl2fastq required for the cellranger mkfastq module and was therefore added to the cellranger dockerfile. Further, cellranger was updated to the latest version, 6.1.2., with naming and containers across cellranger modules updated accordingly. * chore: add bcl2fastq zip to .gitignore * style: fix code linting error * test(cellranger): Add tiles to mkfastq * additional dockerfile for mkfastq * update readme and dockerfiles * update readme * fix: update container for mkfastq * docs: correct typos in readme * test: update md5sum following cellranger update * test: update md5sum following cellranger update * fix: new line for external args in mkfastq * test: update mkfastq tiles argument * test: comment out mkfastq tests until smaller test data found * test: stub-run mkfastq test until smaller test data found * test: fix incorrect file path for mkfastq Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com> Co-authored-by: ggabernet <gisela.gabernet@qbic.uni-tuebingen.de> Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>
31 lines
762 B
Text
31 lines
762 B
Text
process CELLRANGER_MKGTF {
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tag "$gtf"
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label 'process_low'
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if (params.enable_conda) {
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exit 1, "Conda environments cannot be used when using the Cell Ranger tool. Please use docker or singularity containers."
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}
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container "nfcore/cellranger:6.1.2"
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input:
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path gtf
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output:
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path "*.filtered.gtf", emit: gtf
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path "versions.yml" , emit: versions
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script:
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def args = task.ext.args ?: ''
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"""
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cellranger \\
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mkgtf \\
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$gtf \\
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${gtf.baseName}.filtered.gtf \\
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$args
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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cellranger: \$(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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