A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

<!channel> v2 of <#C062H82UCRG|> has just been released!

This is mostly fixing a bunch of sort of major bugs related to Kraken2/Bracken and DIAMOND, but also includes support for building of databases for two more tools - sylph and sourmash, and documents how to build databases that have just a single FASTA.

An important deprecation is the removal of the automatic building of database `tar` archives due to a range of incompatibilities between kraken/bracken vs nextflow vs containers, but I don't think it will be a huge loss - and I also wrote documentation how to do it manually in the FAQ :)

Otherwise thanks to <@UUK6QL2V7> <@U015PB15C5U> <@U02GS5HK553> '@ellmagu' for the help and contributions to this one!

CHANGELOG:

### `Added`

• <https://github.com/nf-core/createtaxdb/pull/108|#108> - Document workaround for building databases from single FASTA files, e.g. from NCBI RefSeq (by @pcantalupo)
• <https://github.com/nf-core/createtaxdb/pull/111|#111> - Added sourmash reference building both for genomes and proteomes (by @Midnighter).
• <https://github.com/nf-core/createtaxdb/pull/117|#117> - Updated to nf-core/tools template 3.4.1 (by @jfy133)
• <https://github.com/nf-core/createtaxdb/pull/124|#124> - Added sylph reference building (by @jfy133 and @sofstam).
### `Fixed`

• <https://github.com/nf-core/createtaxdb/pull/110|#110> - Corrected the documented structures of the grouped output from the `PREPROCESSING` subworkflow
  (by @Midnighter).
• <https://github.com/nf-core/createtaxdb/pull/121|#121> - Fix Kraken2 build failing with local files due to symlink-in-symlink mounting error with containers (:heart: to @ellmagu for reporting, fix by @jfy133)
• <https://github.com/nf-core/createtaxdb/pull/122|#122> - Update DIAMOND to support more recent versions of NCBI taxonomy (by @jfy133)
• <https://github.com/nf-core/createtaxdb/pull/123|#123> - Fix a MALT build validation check incorrectly assigned to --build_krakenuniq (by @jfy133)
• <https://github.com/nf-core/createtaxdb/pull/133|#133> - Fix Kaiju compatible renamed FASTA files being always published even if --kaiju_keepintermediates false (by @jfy133)
### `Dependencies`

| Tool     | Old Version | New Version |
| -------- | ----------- | ----------- |
| sourmash |             | 4.9.4       |
| sylph    |             | 0.9.0       |
| kraken2  | 2.1.5       | 2.1.6       |
| tar      | 1.34        |             |
| nf-core  | 3.3.2       | 3.4.1       |
| DIAMOND  | 2.1.12      | 2.1.16      |
| MultiQC  | 1.31        | 1.32        |
| Nextflow | 24.04.2     | 25.04.2     |

### `Deprecated`

• <https://github.com/nf-core/createtaxdb/pull/118|#118> - Deprecated automated building of `tar.gz` archives of all databases (by @jfy133)
• <https://github.com/nf-core/createtaxdb/pull/126|#126> - Remove guidance about needed double and single quotes when giving to `--&lt;tool&gt;_build_options` as actually not necessary (by @jfy133)
