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a0443e2c54
* Update main.nf * Update meta.yml * Re-add logos as not staged in a way that works with MultiQC config files * Update main.nf * Remove now unnecessary input channel * Remove unused channel from tests * Update hAMRonization to 1.1.1 and add hAMRonization farGene * Fix hamronizatio ntests * Prettier * Fix fargene linting * Correct file * Fix fargene output * Apply suggestions from code review Co-authored-by: Jasmin F <73216762+jasmezz@users.noreply.github.com> * Fix summarise tests * Prettier * Fix incorrect quotes in tags Co-authored-by: Jasmin F <73216762+jasmezz@users.noreply.github.com>
36 lines
882 B
Text
36 lines
882 B
Text
process CELLRANGER_MKREF {
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tag "$fasta"
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label 'process_high'
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if (params.enable_conda) {
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exit 1, "Conda environments cannot be used when using the Cell Ranger tool. Please use docker or singularity containers."
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}
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container "nfcore/cellranger:7.0.0"
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input:
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path fasta
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path gtf
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val reference_name
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output:
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path "${reference_name}", emit: reference
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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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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mkref \\
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--genome=$reference_name \\
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--fasta=$fasta \\
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--genes=$gtf
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cat <<-END_VERSIONS > versions.yml
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"${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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