Subsample fastq
meta :map
Groovy Map containing sample information e.g. [ id:‘test’ ]
ch_reads :file
List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively.
ch_genome_fasta :file
Genome fasta file
Path to genome sequence in fasta format
ch_transcript_fasta :file
Transcript fasta file
Path to transcript sequence in fasta format
ch_gtf :file
GTF features file
Path features in GTF format
ch_index :file
Salmon index files
Directory containing Salmon index
make_index :boolean
Whether to create salmon index before running salmon quant
index :directory
Directory containing salmon index
salmon
reads :file
Subsampled fastq reads.
*.{fq,fastq}{,.gz}
results :directory
Folder containing the quantification results for a specific sample
${prefix}
json_info :file
File containing meta information from Salmon quant Which could be used to infer strandedness among other things
*info.json
versions :file
File containing software versions
versions.yml
