Merge branch 'dev' of github.com:nf-core/createtaxdb into dev

Author: jfy133

.nf-core.yml

@@ -15,4 +15,4 @@ template:
   skip_features:
     - fastqc
     - igenomes
-  version: 3.1.0dev
+  version: 3.1.0

CHANGELOG.md

@@ -3,42 +3,47 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## v3.1.0dev - [unreleased]
+## v3.1.0 - Seductive Siren - [2026-06-03]
 
 ### `Added`
 
+- [#194](https://github.com/nf-core/createtaxdb/pull/194) - Updated to nf-core template 4.0.2 (by @jfy133)
+- [#195](https://github.com/nf-core/createtaxdb/pull/195) - Added Centrifuger database building support (by @haris18s)
+
 ### `Fixed`
 
-- [#196](https://github.com/nf-core/createtaxdb/pull/169) Improved KrakenUniq build clean up step (by @mahesh-panchal, @jfy133)
+- [#196](https://github.com/nf-core/createtaxdb/pull/169) - Improved KrakenUniq build clean up step (by @mahesh-panchal, @jfy133)
 
 ### `Dependencies`
 
-| Tool | Old Version | New Version |
-| ---- | ----------- | ----------- |
-|      |             |             |
+| Tool             | Old Version | New Version |
+| ---------------- | ----------- | ----------- |
+| nf-core template | 4.0.1       | 4.0.2       |
+| nf-schema        | 2.5.1       | 2.7.2       |
+| Centrifuger      |             | 1.1.0       |
 
 ## v3.0.0 - Mystical Medusa - [2026-04-30]
 
 ### `Added`
 
-- [#169](https://github.com/nf-core/createtaxdb/pull/169) Have KAIJU_MKFMI module also export relevant taxdump files for downstream processes (by @jfy133)
-- [#170](https://github.com/nf-core/createtaxdb/pull/170) Publish sometimes generated `unmapped.txt` file for Kraken2 databases (❤️ to @softstam for reporting, fix @jfy133)
-- [#178](https://github.com/nf-core/createtaxdb/pull/178) Add additional validation checks for required MetaCache inputs (by @jfy133)
-- [#179](https://github.com/nf-core/createtaxdb/pull/179) Add new parameter `--save_uncompressed_fastas` to only optionally save decompressed input files (fix @jfy133)
+- [#169](https://github.com/nf-core/createtaxdb/pull/169) - Have KAIJU_MKFMI module also export relevant taxdump files for downstream processes (by @jfy133)
+- [#170](https://github.com/nf-core/createtaxdb/pull/170) - Publish sometimes generated `unmapped.txt` file for Kraken2 databases (❤️ to @softstam for reporting, fix @jfy133)
+- [#178](https://github.com/nf-core/createtaxdb/pull/178) - Add additional validation checks for required MetaCache inputs (by @jfy133)
+- [#179](https://github.com/nf-core/createtaxdb/pull/179) - Add new parameter `--save_uncompressed_fastas` to only optionally save decompressed input files (fix @jfy133)
 
 ### `Fixed`
 
-- [#158](https://github.com/nf-core/createtaxdb/pull/158) Prevent sylph failing due to too long commands when many input genomes (by @softstam, @jfy133)
-- [#160](https://github.com/nf-core/createtaxdb/pull/160) Prevent sourmash failing due to too long commands when many input genomes (by @softstam, @jfy133)
-- [#161](https://github.com/nf-core/createtaxdb/pull/161) Force METACACHE_BUILD module to always use one CPU, as not multi-threaded, removing warning (by @jfy133)
-- [#162](https://github.com/nf-core/createtaxdb/pull/162) Fix links to FAQ in parameter docs (by @jfy133)
-- [#163](https://github.com/nf-core/createtaxdb/pull/163) Fix code block title in auxiliary files section of FAQ (by @jfy133)
-- [#165](https://github.com/nf-core/createtaxdb/pull/165) Force use of KrakenUniq `--jellyfish-bin` to ensure more regular execution (by @jfy133)
-- [#173](https://github.com/nf-core/createtaxdb/pull/173) Fix generated downstream samplesheet's Bracken directory name being flipped (by @jfy133)
-- [#175](https://github.com/nf-core/createtaxdb/pull/175) Fix MetaCache receiving wrong taxonomy file (was seq2map, should have been accession2taxid) (by @sofstam, @jfy133)
-- [#182](https://github.com/nf-core/createtaxdb/pull/182) KMCP emits correct taxonomy files for downstream use (by @sofstam, @jfy133)
-- [#183](https://github.com/nf-core/createtaxdb/pull/183) Fix KrakenUniq using incorrectly non-renamed seqid2map taxonomy file, resulting in no taxonomy info during classification (by @jfy133)
-- [#184](https://github.com/nf-core/createtaxdb/pull/184) Stop generation of concatenated FASTA file of input files if not needed by selected tools (by @jfy133)
+- [#158](https://github.com/nf-core/createtaxdb/pull/158) - Prevent sylph failing due to too long commands when many input genomes (by @softstam, @jfy133)
+- [#160](https://github.com/nf-core/createtaxdb/pull/160) - Prevent sourmash failing due to too long commands when many input genomes (by @softstam, @jfy133)
+- [#161](https://github.com/nf-core/createtaxdb/pull/161) - Force METACACHE_BUILD module to always use one CPU, as not multi-threaded, removing warning (by @jfy133)
+- [#162](https://github.com/nf-core/createtaxdb/pull/162) - Fix links to FAQ in parameter docs (by @jfy133)
+- [#163](https://github.com/nf-core/createtaxdb/pull/163) - Fix code block title in auxiliary files section of FAQ (by @jfy133)
+- [#165](https://github.com/nf-core/createtaxdb/pull/165) - Force use of KrakenUniq `--jellyfish-bin` to ensure more regular execution (by @jfy133)
+- [#173](https://github.com/nf-core/createtaxdb/pull/173) - Fix generated downstream samplesheet's Bracken directory name being flipped (by @jfy133)
+- [#175](https://github.com/nf-core/createtaxdb/pull/175) - Fix MetaCache receiving wrong taxonomy file (was seq2map, should have been accession2taxid) (by @sofstam, @jfy133)
+- [#182](https://github.com/nf-core/createtaxdb/pull/182) - KMCP emits correct taxonomy files for downstream use (by @sofstam, @jfy133)
+- [#183](https://github.com/nf-core/createtaxdb/pull/183) - Fix KrakenUniq using incorrectly non-renamed seqid2map taxonomy file, resulting in no taxonomy info during classification (by @jfy133)
+- [#184](https://github.com/nf-core/createtaxdb/pull/184) - Stop generation of concatenated FASTA file of input files if not needed by selected tools (by @jfy133)
 
 ### `Dependencies`
 
@@ -48,7 +53,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Deprecated`
 
-- [#179](https://github.com/nf-core/createtaxdb/pull/179) The pipeline no longer by default saves decompressed input FASTA files (see new `save_uncompressed_fastas` parameter) (@jfy133)
+- [#179](https://github.com/nf-core/createtaxdb/pull/179) - The pipeline no longer by default saves decompressed input FASTA files (see new `save_uncompressed_fastas` parameter) (@jfy133)
 
 ## v2.1.0 - Gracious Goblin - [2026-02-10]
 

assets/multiqc_config.yml

@@ -1,7 +1,5 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/createtaxdb/tree/dev" target="_blank">nf-core/createtaxdb</a>
-  analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/createtaxdb/dev/docs/output" target="_blank">documentation</a>.
+  This report has been generated by the <a href="https://github.com/nf-core/createtaxdb/releases/tag/3.1.0" target="_blank">nf-core/createtaxdb</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://nf-co.re/createtaxdb/3.1.0/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-createtaxdb-methods-description":
     order: -1000

nextflow.config

@@ -360,7 +360,7 @@ manifest {
     mainScript      = 'main.nf'
     defaultBranch   = 'main'
     nextflowVersion = '!>=25.10.4'
-    version         = '3.1.0dev'
+    version         = '3.1.0'
     doi             = '10.5281/zenodo.15696114'
 }