Extract reads classified at any user-specified taxonomy IDs.
Input
name:type
description
pattern
taxid:string
A list of taxid separated by spaces
meta:map
Groovy Map containing sample information
e.g. [ id:'sample1', single_end:false ]
classified_reads_assignment:file
A file contains the taxonomic classification of each input read.
*.{classifiedreads.txt}
meta:map
Groovy Map containing sample information
e.g. [ id:'sample1', single_end:false ]
classified_reads_fastq:file
Classified reads as belonging to any of the taxa on the kraken2 database.
*.{fastq.gz}
meta:map
Groovy Map containing sample information
e.g. [ id:'sample1', single_end:false ]
report:file
Optional Kraken2 report containing stats about classified and not classified reads.
*.{report.txt}
Output
name:type
description
pattern
extracted_kraken2_reads
meta:map
Groovy Map containing sample information
e.g. [ id:'sample1', single_end:false ]
*.{fastq,fasta}:file
Reads assigned to a taxid list.
*.{fastq,fasta}
versions
versions.yml:file
File containing software versions
versions.yml
Tools
krakentools
GPL v3
KrakenTools is a suite of scripts to be used for post-analysis of Kraken/KrakenUniq/Kraken2/Bracken results. Please cite the relevant paper if using KrakenTools with any of the listed programs.
