gene/transcript quantification with Salmon
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
results
meta:directory
Folder containing the quantification results for a specific sample
${prefix}
${prefix}:directory
json_info
meta:file
File containing meta information from Salmon quant
*info.json
*info.json:file
lib_format_counts
*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
Salmon is a tool for wicked-fast transcript quantification from RNA-seq data
