Classifies metagenomic sequence data
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
reads{:bash}
:file
List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively.
db{:bash}
:directory
Kraken2 database
save_output_fastqs{:bash}
:string
If true, optional commands are added to save classified and unclassified reads as fastq files
save_reads_assignment{:bash}
If true, an optional command is added to save a file reporting the taxonomic classification of each input read
classified_reads_fastq{:bash}
*.classified{.,_}*{:bash}
Reads classified as belonging to any of the taxa on the Kraken2 database.
*{fastq.gz}
unclassified_reads_fastq{:bash}
*.unclassified{.,_}*{:bash}
Reads not classified to any of the taxa on the Kraken2 database.
classified_reads_assignment{:bash}
*classifiedreads.txt{:bash}
Kraken2 output file indicating the taxonomic assignment of each input read
report{:bash}
*report.txt{:bash}
Kraken2 report containing stats about classified and not classified reads.
*.{report.txt}
versions{:bash}
versions.yml{:bash}
File containing software versions
versions.yml
Kraken2 is a taxonomic sequence classifier that assigns taxonomic labels to sequence reads
