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

]

sequences:file

List of input files containing sequences. All of them must be either in FASTA or FASTQ format.

prefixes:string

List of sample identifiers or filename prefixes. Must correspond in order and length to the ‘sequences’, or to the number of sequencing pairs.

sequence_type:string

Format of all given sequencing files as literal string, either ‘fasta’ or ‘fastq’.

{fasta,fastq}

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_reads:boolean

Optionally, commands are added to save classified and unclassified reads as FASTQ or FASTA files depending on the input format. When the input is paired-end, the single output FASTQ contains merged reads.

report_file:boolean

Whether to generate a report of relative abundances.

save_output:boolean

Whether to save a file reporting the taxonomic classification of each input read.

Output

name:type
description
pattern

classified_reads

meta:map

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

]

*.classified.${sequence_type}.gz:file

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

*.classified.{fastq,fasta}.gz

unclassified_reads

meta:map

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

]

*.unclassified.${sequence_type}.gz:file

Reads not classified to any of the taxa in the KrakenUniq reference database.

*.unclassified.{fastq,fasta}.gz

classified_assignment

meta:map

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

]

*.krakenuniq.classified.txt:file

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

*.krakenuniq.classified.txt

report

meta:map

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

]

*.krakenuniq.report.txt:file

KrakenUniq report containing statistics about classified and unclassified reads.

*.krakenuniq.report.txt

versions

versions.yml:file

File containing software versions

versions.yml

Tools

krakenuniq
MIT

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