Description

gene/transcript quantification with Salmon

Input

name:type
description
pattern

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

reads:file

List of input FastQ files for single-end or paired-end data. Multiple single-end fastqs or pairs of paired-end fastqs are handled.

index:directory

Folder containing the star index files

gtf:file

GTF of the reference transcriptome

transcript_fasta:file

Fasta file of the reference transcriptome

alignment_mode:boolean

whether to run salmon in alignment mode

lib_type:string

Override library type inferred based on strandedness defined in meta object

Output

name:type
description
pattern

results

meta:directory

Folder containing the quantification results for a specific sample

${prefix}

${prefix}:directory

Folder containing the quantification results for a specific sample

${prefix}

json_info

meta:file

File containing meta information from Salmon quant

*info.json

*info.json:file

File containing meta information from Salmon quant

*info.json

lib_format_counts

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

*lib_format_counts.json:file

File containing the library format counts

*lib_format_counts.json

versions

versions.yml:file

File containing software versions

versions.yml

Tools

salmon
GPL-3.0-or-later

Salmon is a tool for wicked-fast transcript quantification from RNA-seq data