nf-core/createtaxdb

Parallelised and automated construction of metagenomic classifier databases of different tools

databasedatabase-buildermetagenomic-profilingmetagenomicsprofilingtaxonomic-profiling

Version history

#169 Have KAIJU_MKFMI module also export relevant taxdump files for downstream processes (by @jfy133)
#170 Publish sometimes generated unmapped.txt file for Kraken2 databases (❤️ to @softstam for reporting, fix @jfy133)
#178 Add additional validation checks for required MetaCache inputs (by @jfy133)
#179 Add new parameter --save_uncompressed_fastas to only optionally save decompressed input files (fix @jfy133)

#158 Prevent sylph failing due to too long commands when many input genomes (by @softstam, @jfy133)
#160 Prevent sourmash failing due to too long commands when many input genomes (by @softstam, @jfy133)
#161 Force METACACHE_BUILD module to always use one CPU, as not multi-threaded, removing warning (by @jfy133)
#162 Fix links to FAQ in parameter docs (by @jfy133)
#163 Fix code block title in auxiliary files section of FAQ (by @jfy133)
#165 Force use of KrakenUniq --jellyfish-bin to ensure more regular execution (by @jfy133)
#173 Fix generated downstream samplesheet’s Bracken directory name being flipped (by @jfy133)
#175 Fix MetaCache receiving wrong taxonomy file (was seq2map, should have been accession2taxid) (by @sofstam, @jfy133)
#182 KMCP emits correct taxonomy files for downstream use (by @sofstam, @jfy133)
#183 Fix KrakenUniq using incorrectly non-renamed seqid2map taxonomy file, resulting in no taxonomy info during classification (by @jfy133)
#184 Stop generation of concatenated FASTA file of input files if not needed by selected tools (by @jfy133)

Tool	Old Version	New Version

#117 - Updated to nf-core/tools template 3.5.1 (by @jfy133)
#143 - Documented how to resovle KrakenUniq unbound variable jellyfish issue (❤️ to @flass for suggesting, added by @jfy133)
#140 - Added MetaCache database building support (❤️ to @ChillarAnand for suggestion, added by @alxndrdiaz and @jfy133)
#144 - Added tutorial on how to convert an NCBI assembly_summary.txt file to input samplesheet (❤️ to @dialvarezs for improvements, by @jfy133)

Tool	Old Version	New Version
nf-core	3.4.1	3.5.1
MetaCache		2.5.0

#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.