mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-11 04:33:10 +00:00
e745e167c1
* fix yml formatting * allow fastq.gz and fq.gz as file input, add meta.yml and test * fix yaml files * Revert "allow fastq.gz and fq.gz as file input, add meta.yml and test" This reverts commit 34002d7a7a8c7f7bb4600c3377f35c87849f71a4. * prettier magic! * fix comments for yamllint * remove node version number * fix linting errors Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
56 lines
1.5 KiB
YAML
56 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
|
|
licence: ["GPL-3.0-or-later"]
|
|
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}"
|
|
- versions:
|
|
type: file
|
|
description: File containing software versions
|
|
pattern: "versions.yml"
|
|
|
|
authors:
|
|
- "@kevinmenden"
|
|
- "@drpatelh"
|