Description

Produces a contamination report from FastQ input after subsampling

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

reads (file)

List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively

sample_size (string)

Number of reads to subsample for contamination detection.

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

report (file)

Kraken2 contamination report

*.txt

versions (file)

File containing software versions

versions.yml