Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
reads
:file
List of input FastQ files for single-end or paired-end data, or a
single BAM of reads already aligned to the transcriptome (a .bam
extension switches the module into salmon’s alignment mode). Pass
--libType via ext.args to select a specific library type;
salmon auto-detects it otherwise.
meta2
:map
Groovy Map containing reference information
e.g. [ id:‘genome’ ]
index
:directory
Folder containing the salmon index files. Required for reads
mode; pass [] in alignment mode.
gtf
:file
GTF of the reference transcriptome
transcript_fasta
:file
Fasta file of the reference transcriptome. Required in alignment
mode as the -t reference; pass [] in reads mode.
Output
name:type
description
pattern
results
meta
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
${prefix}
:directory
Folder containing the quantification results for a specific sample
${prefix}
json_info
meta
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*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:false ]
*lib_format_counts.json
:file
File containing the library format counts
*lib_format_counts.json
versions_salmon
${task.process}
:string
The process the versions were collected from
salmon
:string
The tool name
salmon --version | sed -e "s/salmon //g"
:eval
The expression to obtain the version of the tool
Topics
name:type
description
pattern
versions
${task.process}
:string
The process the versions were collected from
salmon
:string
The tool name
salmon --version | sed -e "s/salmon //g"
:eval
The expression to obtain the version of the tool
Tools
salmon
GPL-3.0-or-later
Salmon is a tool for wicked-fast transcript quantification from RNA-seq data
