gene/transcript quantification with Salmon
meta
Groovy Map containing sample information e.g. [ id:‘test’, single_end
reads
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
Folder containing the star index files
gtf
GTF of the reference transcriptome
transcript_fasta
Fasta file of the reference transcriptome
alignment_mode
whether to run salmon in alignment mode
lib_type
Override library type inferred based on strandedness defined in meta object
results
Folder containing the quantification results for a specific sample
${prefix}
json_info
File containing meta information from Salmon quant
*info.json
versions
File containing software versions
versions.yml
Salmon is a tool for wicked-fast transcript quantification from RNA-seq data
