gene/transcript quantification with Salmon
meta
:map
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. Multiple single-end fastqs or pairs of paired-end fastqs are handled.
index
:directory
Folder containing the star index files
gtf
GTF of the reference transcriptome
transcript_fasta
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
results
Folder containing the quantification results for a specific sample
${prefix}
json_info
*info.json
File containing meta information from Salmon quant
lib_format_counts
*lib_format_counts.json
File containing the library format counts
versions_salmon
${task.process}
The process the versions were collected from
salmon
The tool name
salmon --version | sed -e "s/salmon //g"
:eval
The expression to obtain the version of the tool
versions
Salmon is a tool for wicked-fast transcript quantification from RNA-seq data
