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* feat(cellranger): Add initial count module Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com> * feat(cellranger): Add mkgtf module * test(cellranger): Fix count test with mkgtf * fix(cellranger): Generalize gtf attribute filters * chore: Add .gitignore for cellranger tar * build(cellranger): Update dockerfile https://joshtronic.com/2021/09/12/fixed-repository-debian-security-buster-updates-changed-suite-from-stable-to-oldstable/ * Apply suggestions from code review Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com> * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/cellranger/mkgtf/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * style: Capitalize README * test(cellranger): Update pytest_modules * feat(cellranger): Add initial mkfastq module * ci: Update pytest modules * refactor(cellranger): Update modules to new syntax * docs(cellranger): Update meta files There is some terrible copy-pasting going on. * fix(cellranger): Add args Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
49 lines
1.4 KiB
Text
49 lines
1.4 KiB
Text
process CELLRANGER_COUNT {
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tag "$meta.gem"
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label 'process_high'
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if (params.enable_conda) {
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exit 1, "Conda environments cannot be used when using the Cell Ranger tool. Please use docker or singularity containers."
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}
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container "nfcore/cellranger:6.0.2"
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input:
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tuple val(meta), path(reads)
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path reference
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output:
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path("sample-${meta.gem}/outs/*"), emit: outs
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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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def sample_arg = meta.samples.unique().join(",")
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def reference_name = reference.name
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"""
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cellranger \\
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count \\
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--id='sample-${meta.gem}' \\
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--fastqs=. \\
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--transcriptome=$reference_name \\
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--sample=$sample_arg \\
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--localcores=$task.cpus \\
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--localmem=${task.memory.toGiga()} \\
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$args
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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cellranger: \$(echo \$( cellranger --version 2>&1) | sed 's/^.*[^0-9]\\([0-9]*\\.[0-9]*\\.[0-9]*\\).*\$/\\1/' )
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END_VERSIONS
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"""
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stub:
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"""
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mkdir -p "sample-${meta.gem}/outs/"
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touch sample-${meta.gem}/outs/fake_file.txt
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cat <<-END_VERSIONS > versions.yml
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"${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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