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.
seqid2taxid.map
Output
name:type
description
pattern
library_added_files
meta:map
Groovy Map containing sample information
e.g. [ id:'sample1', single_end:false ]
*/
${prefix}/library/added/*:file
Files present in the /library/added/ directory, including FASTA files, masked FASTAs, and prelim_map files.
*
seqid2taxid_map
meta:map
Groovy Map containing sample information
e.g. [ id:'sample1', single_end:false ]
*/
${prefix}/seqid2taxid.map:file
File mapping sequence IDs to taxonomy IDs, either generated or premade.
seqid2taxid.map
taxonomy_files
meta:map
Groovy Map containing sample information
e.g. [ id:'sample1', single_end:false ]
*/
${prefix}/taxonomy/*:file
Files present in the /taxonomy/ directory, including nodes.dmp, names.dmp, and .accession2taxid files.
*
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.
