nf-core_modules/modules/cellranger/mkgtf/meta.yml
Edmund Miller e2ba70ed9a
Add Cell Ranger mkfastq, mkgtf, and count (#979)
* 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>
2021-12-02 14:27:20 +00:00

31 lines
1.2 KiB
YAML

name: cellranger_mkgtf
description: Module to build a filtered gtf needed by the 10x Genomics Cell Ranger tool. Uses the cellranger mkgtf 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:
- gtf:
type: file
description:
pattern: "*.gtf"
output:
- gtf:
type: folder
description: gtf transcriptome file
pattern: "*.filtered.gtf"
- versions:
type: file
description: File containing software version
pattern: "versions.yml"
authors:
- "@ggabernet"
- "@Emiller88"