nf-core_modules/modules/salmon/quant/meta.yml

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name: salmon_quant
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description: gene/transcript quantification with Salmon
keywords:
- index
- fasta
- genome
- reference
tools:
- salmon:
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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
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output:
- sample_output:
type: directory
description: Folder containing the quantification results for a specific sample
pattern: "${prefix}"
- versions:
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type: file
description: File containing software versions
pattern: "versions.yml"
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authors:
- "@kevinmenden"
- "@drpatelh"