Description

Subsample fastq

Input

Name (Type)
Description
Pattern

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

Output

Name (Type)
Description
Pattern

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