nf-core/createtaxdb

Parallelised and automated construction of metagenomic classifier databases of different tools

databasedatabase-buildermetagenomic-profilingmetagenomicsprofilingtaxonomic-profiling

Version history

#108 - Document workaround for building databases from single FASTA files, e.g. from NCBI RefSeq (by @pcantalupo)
#111 - Added sourmash reference building both for genomes and proteomes (by @Midnighter).
#117 - Updated to nf-core/tools template 3.4.1 (by @jfy133)
#124 - Added sylph reference building (by @jfy133 and @sofstam).

#110 - Corrected the documented structures of the grouped output from the PREPROCESSING subworkflow (by @Midnighter).
#121 - Fix Kraken2 build failing with local files due to symlink-in-symlink mounting error with containers (❤️ to @ellmagu for reporting, fix by @jfy133)
#122 - Update DIAMOND to support more recent versions of NCBI taxonomy (by @jfy133)
#123 - Fix a MALT build validation check incorrectly assigned to —build_krakenuniq (by @jfy133)
#133 - Fix Kaiju compatible renamed FASTA files being always published even if —kaiju_keepintermediates false (by @jfy133)

#118 - Deprecated automated building of tar.gz archives of all databases (by @jfy133)
#126 - Remove guidance about needed double and single quotes when giving to --<tool>_build_options as actually not necessary (by @jfy133)

Initial release of nf-core/createtaxdb, created with the nf-core template.

Adds database building support for the following tools:

(Primarily) nucleotide based
- Bracken (added by @alxndrdiaz)
- Centrifuge (added by @jfy133)
- ganon (added by @jfy133)
- KMCP (added by @alxndrdiaz)
- KrakenUniq (added by @jfy133)
- Kraken2 (added by @alxndrdiaz)
- MALT (added by @jfy133 and @LilyAnderssonLee)
(Primarily) protein based
- DIAMOND (added by @jfy133)
- Kaiju (added by @jfy133)

Additional optimisation when running with very large number of genomes by @BioWilko.