Groovy Map containing sample information
e.g. [ id:'sample1', single_end:false ]
fasta:file
fasta file that will be added to the database
*.{fa,fasta,fna,ffn}
taxonomy_names:file
used for associating sequences with taxonomy IDs
*.dmp
taxonomy_nodes:file
tree nodes using NCBI taxonomy nomenclature
*.dmp
accession2taxid:file
associates sequence accession IDs to taxonomy IDs
*.accession2taxid
seqid2taxid:file
optional premade 2 column seq2taxid map file. Must be named seq2taxid.map. If not supplied will be generated by kraken2 itself during upstream build step.
seqit2taxid.map
Output
name:type
description
pattern
db
meta:map
Groovy Map containing sample information
e.g. [ id:'sample1', single_end:false ]
*/
${prefix}:directory
Contains required files to build the database
*/
versions
versions.yml:file
File containing software versions
versions.yml
Tools
kraken2
MIT
Kraken2 is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies.
