mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-13 05:13:09 +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>
37 lines
1.4 KiB
YAML
37 lines
1.4 KiB
YAML
name: cellranger_mkref
|
|
description: Module to build the reference needed by the 10x Genomics Cell Ranger tool. Uses the cellranger mkref command.
|
|
keywords:
|
|
- reference
|
|
- mkref
|
|
- index
|
|
tools:
|
|
- cellranger:
|
|
description: Cell Ranger by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more.
|
|
homepage: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger
|
|
documentation: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov
|
|
tool_dev_url: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov
|
|
doi: ""
|
|
licence: 10x Genomics EULA
|
|
input:
|
|
- fasta:
|
|
type: file
|
|
description: fasta genome file
|
|
pattern: "*.{fasta,fa}"
|
|
- gtf:
|
|
type: file
|
|
description: gtf transcriptome file
|
|
pattern: "*.gtf"
|
|
- reference_name:
|
|
type: val
|
|
description: name to give the reference folder
|
|
pattern: str
|
|
output:
|
|
- reference:
|
|
type: folder
|
|
description: Folder containing all the reference indices needed by Cell Ranger
|
|
- versions:
|
|
type: file
|
|
description: File containing software version
|
|
pattern: "versions.yml"
|
|
authors:
|
|
- "@ggabernet"
|