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 ]
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:false ]
*.classified.${sequence_type}.gz:file
Reads classified as belonging to any of the taxa
in the KrakenUniq reference database.
*.classified.{fastq,fasta}.gz
unclassified_reads
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.unclassified.${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:false ]
*.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:false ]
*.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
