mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-10 20:23:10 +00:00
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>
27 lines
1 KiB
Text
27 lines
1 KiB
Text
process {
|
|
|
|
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
|
|
|
|
withName: CELLRANGER_MKGTF {
|
|
ext.args = '--attribute=gene_biotype:protein_coding \
|
|
--attribute=gene_biotype:lincRNA \
|
|
--attribute=gene_biotype:antisense \
|
|
--attribute=gene_biotype:IG_LV_gene \
|
|
--attribute=gene_biotype:IG_V_gene \
|
|
--attribute=gene_biotype:IG_V_pseudogene \
|
|
--attribute=gene_biotype:IG_D_gene \
|
|
--attribute=gene_biotype:IG_J_gene \
|
|
--attribute=gene_biotype:IG_J_pseudogene \
|
|
--attribute=gene_biotype:IG_C_gene \
|
|
--attribute=gene_biotype:IG_C_pseudogene \
|
|
--attribute=gene_biotype:TR_V_gene \
|
|
--attribute=gene_biotype:TR_V_pseudogene \
|
|
--attribute=gene_biotype:TR_D_gene \
|
|
--attribute=gene_biotype:TR_J_gene \
|
|
--attribute=gene_biotype:TR_J_pseudogene \
|
|
--attribute=gene_biotype:TR_C_gene'
|
|
|
|
|
|
}
|
|
|
|
}
|