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