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e2ba70ed9a
* 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>
31 lines
1.1 KiB
Text
31 lines
1.1 KiB
Text
process {
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publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
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withName: CELLRANGER_MKGTF {
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ext.args = '--attribute=gene_biotype:protein_coding \
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--attribute=gene_biotype:lincRNA \
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--attribute=gene_biotype:antisense \
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--attribute=gene_biotype:IG_LV_gene \
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--attribute=gene_biotype:IG_V_gene \
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--attribute=gene_biotype:IG_V_pseudogene \
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--attribute=gene_biotype:IG_D_gene \
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--attribute=gene_biotype:IG_J_gene \
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--attribute=gene_biotype:IG_J_pseudogene \
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--attribute=gene_biotype:IG_C_gene \
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--attribute=gene_biotype:IG_C_pseudogene \
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--attribute=gene_biotype:TR_V_gene \
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--attribute=gene_biotype:TR_V_pseudogene \
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--attribute=gene_biotype:TR_D_gene \
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--attribute=gene_biotype:TR_J_gene \
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--attribute=gene_biotype:TR_J_pseudogene \
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--attribute=gene_biotype:TR_C_gene'
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}
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withName: CELLRANGER_COUNT {
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ext.args = '--chemistry SC3Pv3'
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}
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}
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