nf-core_modules/modules/salmon/quant/meta.yml
Matthias Hörtenhuber e745e167c1
Fix formatting in yaml files, add yamllint config (#1279)
* 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>
2022-02-15 11:15:27 +00:00

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"