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