mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 07:42:05 +00:00
e937c7950a
* Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
55 lines
1.5 KiB
YAML
55 lines
1.5 KiB
YAML
name: salmon_quant
|
|
description: gene/transcript quantification with Salmon
|
|
keywords:
|
|
- index
|
|
- fasta
|
|
- genome
|
|
- reference
|
|
tools:
|
|
- salmon:
|
|
description: |
|
|
Salmon is a tool for wicked-fast transcript quantification from RNA-seq data
|
|
homepage: https://salmon.readthedocs.io/en/latest/salmon.html
|
|
manual: https://salmon.readthedocs.io/en/latest/salmon.html
|
|
doi: 10.1038/nmeth.4197
|
|
input:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test', single_end:false ]
|
|
- reads:
|
|
type: file
|
|
description: |
|
|
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
|
|
respectively.
|
|
- index:
|
|
type: directory
|
|
description: Folder containing the star index files
|
|
- gtf:
|
|
type: file
|
|
description: GTF of the reference transcriptome
|
|
- transcriptome_fasta:
|
|
type: file
|
|
description: Fasta file of the reference transcriptome
|
|
- alignment_mode:
|
|
type: boolean
|
|
description: whether to run salmon in alignment mode
|
|
- lib_type:
|
|
type: string
|
|
description: |
|
|
Override library type inferred based on strandedness defined in meta object
|
|
|
|
output:
|
|
- sample_output:
|
|
type: directory
|
|
description: Folder containing the quantification results for a specific sample
|
|
pattern: "${prefix}"
|
|
- version:
|
|
type: file
|
|
description: File containing software version
|
|
pattern: "*.{version.txt}"
|
|
|
|
authors:
|
|
- "@kevinmenden"
|
|
- "@drpatelh"
|