Description

Classifies metagenomic sequence data using unique k-mer counts

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]

fastqs (file)

List of input FastQ files

db (directory)

KrakenUniq database

ram_chunk_size (string)

Amount of maximum amount of RAM each chunk of database that should be loaded at any one time

*GB

save_output_fastqs (boolean)

If true, optional commands are added to save classified and unclassified reads
as fastq files

save_reads_assignment (boolean)

If true, an optional command is added to save a file reporting the taxonomic
classification of each input read

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]

classified_reads_fastq (file)

Reads classified as belonging to any of the taxa
on the KrakenUniq database.

*.fastq.gz

unclassified_reads_fastq (file)

Reads not classified to any of the taxa
on the KrakenUniq database.

*.fastq.gz

classified_assignment (file)

KrakenUniq output file indicating the taxonomic assignment of
each input read ## DOUBLE CHECK!!

report (file)

KrakenUniq report containing stats about classified
and not classifed reads.

*.report.txt

versions (file)

File containing software versions

versions.yml

Tools

krakenuniq
MIT

Metagenomics classifier with unique k-mer counting for more specific results