Version bump for v5.2.0 release [Puce Pangolin]

.nf-core.yml

@@ -16,4 +16,4 @@ template:
   name: mag
   org: nf-core
   outdir: .
-  version: 5.2.0dev
+  version: 5.2.0

CHANGELOG.md

@@ -3,14 +3,19 @@
 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).
 
-## v5.1.0dev - [date]
+## v5.2.0 - Puce Pangolin [2025-11-07]
 
 ### `Added`
 
+- [#842](https://github.com/nf-core/mag/pull/842) - Add support for running multiple binQC tools in one run using dedicated `--run_busco`, `--run_checkm`, and `--run_checkm2` parameters (by @harper357, with contributions from @dialvarezs, @prototaxites and @jfy133)
 - [#881](https://github.com/nf-core/mag/pull/881) - Add binner MetaBinner (by @d4straub, insprired by @HeshamAlmessady & @AlphaSquad)
 
 ### `Changed`
 
+- [#842](https://github.com/nf-core/mag/pull/842) - Change `bin_summary.tsv` format for improved clarity and more comprehensiveness (by @harper357, with contributions from @dialvarezs, @prototaxites and @jfy133)
+  - Now will include columns from all bin QC tools executed in a given run (i.e., all/any of BUSCO, CheckM and CheckM2)
+  - Adds suffixes to all columns (`_<toolname>`) to distinguish which column comes from which tool
+
 ### `Fixed`
 
 - [#896](https://github.com/nf-core/mag/pull/896) - Remove obsolete execution command from README (by @dialvarezs)
@@ -26,21 +31,19 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Deprecated`
 
-## v5.1.0 - 2025-10-27
+- [#842](https://github.com/nf-core/mag/pull/842) - Remove `--binqc_tool` (by @harper357, with contributions from @dialvarezs, @prototaxites and @jfy133)
+
+## v5.1.0 - Platinum Pudu [2025-10-27]
 
 ### `Added`
 
 - [#873](https://github.com/nf-core/mag/pull/873) - Document usage of `longread_percentidentity` and `shortread_percentidentity` and set the value of `longread_percentidentity` in the `test_full` profile to 85 (by @prototaxites)
-- [#842](https://github.com/nf-core/mag/pull/842) - Add support for running multiple binQC tools in one run using dedicated `--run_busco`, `--run_checkm`, and `--run_checkm2` parameters (by @harper357, with contributions from @dialvarezs, @prototaxites and @jfy133)
 - [#875](https://github.com/nf-core/mag/pull/875) - Add binner COMEBin (by @d4straub)
 
 ### `Changed`
 
 - [#878](https://github.com/nf-core/mag/pull/878) - Refine test_full config with optimised resource usage for AWS release megatests (by @jfy133)
 - [#880](https://github.com/nf-core/mag/pull/880) - Updated to nf-core 3.4.1 `TEMPLATE` (by @jfy133)
-- [#842](https://github.com/nf-core/mag/pull/842) - Change `bin_summary.tsv` format for improved clarity and more comprehensiveness (by @harper357, with contributions from @dialvarezs, @prototaxites and @jfy133)
-  - Now will include columns from all bin QC tools executed in a given run (i.e., all/any of BUSCO, CheckM and CheckM2)
-  - Adds suffixes to all columns (`_<toolname>`) to distinguish which column comes from which tool
 
 ### `Fixed`
 
@@ -57,9 +60,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Deprecated`
 
-- [#842](https://github.com/nf-core/mag/pull/842) - Remove `--binqc_tool` (by @harper357, with contributions from @dialvarezs, @prototaxites and @jfy133)
-
-## 5.0.0 - [2025-09-30]
+## v5.0.0 - Green Squirrel [2025-09-30]
 
 ### `Added`
 
@@ -131,7 +132,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#855](https://github.com/nf-core/mag/pull/855) - Remove test_adapterremoval, test_ancient_dna, test_bbnorm, test_busco_auto, test_host_rm, test_hybrid_host_rm, test_binrefinement, test_concoct and test_longread profiles (added by @dialvarezs)
 - [#864](https://github.com/nf-core/mag/pull/864) - Remove `--gtdb_mash` due to dropping of support by GTDBTk itself (by @prototaxites and @jfy133)
 
-## v4.0.0 - [2025-05-22]
+## v4.0.0 - Blue Huemul [2025-05-22]
 
 ### `Added`
 
@@ -167,7 +168,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - [#730](https://github.com/nf-core/mag/pull/730) - Remove `--busco_auto_lineage_prok` due to update and simplified usage of BUSCO (added by @jfy133, @dialvarezs)
 
-## 3.4.0 [2025-04-04]
+## v3.4.0 - Green Gecko [2025-04-04]
 
 ### `Added`
 
@@ -216,7 +217,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Deprecated`
 
-## 3.3.0 [2024-12-19]
+## v3.3.0 - Red Reindeer [2024-12-19]
 
 ### `Added`
 
@@ -251,7 +252,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Deprecated`
 
-## 3.2.1 [2024-10-30]
+## v3.2.1 [2024-10-30]
 
 ### `Added`
 
@@ -265,7 +266,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Deprecated`
 
-## 3.2.0 [2024-10-27]
+## v3.2.0 - Salmon Salmon [2024-10-27]
 
 ### `Added`
 
@@ -297,7 +298,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Deprecated`
 
-## 3.1.0 [2024-10-04]
+## v3.1.0 - Pink Panda [2024-10-04]
 
 ### `Added`
 
@@ -325,7 +326,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - [#670](https://github.com/nf-core/mag/pull/670) - Deprecated `--gtdbtk_pplacer_scratch` due to unintuitive usage (reported by harper357, fixed by @jfy133)
 
-## 3.0.3 [2024-08-27]
+## v3.0.3 [2024-08-27]
 
 ### `Added`
 
@@ -344,7 +345,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Deprecated`
 
-## 3.0.2 [2024-07-04]
+## v3.0.2 [2024-07-04]
 
 ### `Added`
 
@@ -367,7 +368,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Deprecated`
 
-## 3.0.1 [2024-06-10]
+## v3.0.1 [2024-06-10]
 
 ### `Added`
 
@@ -387,7 +388,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Deprecated`
 
-## 3.0.0 - [2024-05-13]
+## v3.0.0 - Magenta Magpie [2024-05-13]
 
 ### `Added`
 
@@ -408,7 +409,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - [#599](https://github.com/nf-core/mag/pull/599) - Direct reads input (`--input 'sample_{R1,R2}.fastq.gz'`) is no longer supported, all input must come via samplesheets (by @jfy133)
 
-## 2.5.4 - [2024-02-12]
+## v2.5.4 [2024-02-12]
 
 ### `Added`
 
@@ -425,7 +426,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Deprecated`
 
-## 2.5.3 - [2024-02-05]
+## v2.5.3 [2024-02-05]
 
 ### `Added`
 
@@ -441,7 +442,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Deprecated`
 
-## 2.5.2 - [2024-02-02]
+## v2.5.2 [2024-02-02]
 
 ### `Added`
 
@@ -466,7 +467,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Deprecated`
 
-## 2.5.1 - [2023-11-17]
+## v2.5.1 [2023-11-17]
 
 ### `Added`
 
@@ -488,7 +489,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - [#536](https://github.com/nf-core/mag/pull/536) - Remove custom function with native Nextflow for checking file extension (reported by @d4straub, fix by @jfy133)
 
-## 2.5.0 - [2023-10-10]
+## 2.5.0 - Aquamarine Kangaroo - [2023-10-10]
 
 ### `Added`
 
@@ -513,7 +514,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - [#504](https://github.com/nf-core/mag/pull/504) - `--busco_reference`, `--busco_download_path`, `--save_busco_reference` parameters have been deprecated and replaced with new parameters (by @gregorysprenger).
 
-## 2.4.0 - 2023-09-26
+## v2.4.0 - Grey Hammerhead [2023-09-26]
 
 ### `Added`
 
@@ -577,7 +578,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#458](https://github.com/nf-core/mag/pull/458) - Correct the major issue in ancient DNA workflow of binning refinement being performed on uncorrected contigs instead of aDNA consensus recalled contigs (issue [#449](https://github.com/nf-core/mag/issues/449))
 - [#451](https://github.com/nf-core/mag/pull/451) - Fix results file overwriting in Ancient DNA workflow (reported by @alexhbnr, fix by @jfy133, and integrated by @maxibor in [#458](https://github.com/nf-core/mag/pull/458) )
 
-## v2.3.0 - [2023/03/02]
+## v2.3.0 - Red Cow [2023-03-02]
 
 ### `Added`
 
@@ -614,7 +615,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 | Freebayes | 1.3.5            | 1.3.6       |
 | SAMtools  | 1.15             | 1.16.1      |
 
-## v2.2.1 - 2022/08/25
+## v2.2.1 [2022-08-25]
 
 ### `Added`
 
@@ -627,7 +628,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Dependencies`
 
-## v2.2.0 - 2022/06/14
+## v2.2.0 - Golden Mammoth [2022-06-14]
 
 ### `Added`
 
@@ -660,7 +661,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 | fastp   | 0.20.1           | 0.23.2      |
 | MultiQC | 1.11             | 1.12        |
 
-## v2.1.1 - 2021/11/25
+## v2.1.1 [2021-11-25]
 
 ### `Added`
 
@@ -683,7 +684,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#255](https://github.com/nf-core/mag/pull/255) - Update gtdbtk conda channel.
 - [#258](https://github.com/nf-core/mag/pull/258) - FastP results are now in MultiQC.
 
-## v2.1.0 - 2021/07/29
+## v2.1.0 - Black Zebra [2021-07-29]
 
 ### `Added`
 
@@ -699,7 +700,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - [#226](https://github.com/nf-core/mag/pull/226) - Fix handling of `BUSCO` output when run in auto lineage selection mode and selected specific lineage is the same as the generic one.
 
-## v2.0.0 - 2021/06/01
+## v2.0.0 - Silver Swan [2021-06-01]
 
 ### `Added`
 
@@ -734,7 +735,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#195](https://github.com/nf-core/mag/pull/195) - Fix documentation regarding required compression of input FastQ files [#160](https://github.com/nf-core/mag/issues/160)
 - [#196](https://github.com/nf-core/mag/pull/196) - Add process for CAT database creation as solution for problem caused by incompatible `DIAMOND` version used for pre-built `CAT database` and `CAT classification` [#90](https://github.com/nf-core/mag/issues/90), [#188](https://github.com/nf-core/mag/issues/188)
 
-## v1.2.0 - 2021/02/10
+## v1.2.0 - Yellow Squirrel [2021-02-10]
 
 ### `Added`
 
@@ -754,7 +755,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - [#143](https://github.com/nf-core/mag/pull/143) - Change parameter: `--manifest` -> `--input`
 
-## v1.1.2 - 2020/11/24
+## v1.1.2 - Blue Panda [2020-11-24]
 
 ### `Changed`
 
@@ -764,7 +765,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - [#133](https://github.com/nf-core/mag/pull/133) - Fixed processing of `--input` parameter [#131](https://github.com/nf-core/mag/issues/131)
 
-## v1.1.1 - 2020/11/10
+## v1.1.1 - Lime Owl [2020-11-10]
 
 ### `Added`
 
@@ -781,7 +782,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#120](https://github.com/nf-core/mag/pull/120) - Fix link to CAT database in help message
 - [#124](https://github.com/nf-core/mag/pull/124) - Fix description of `CAT` process in `output.md`
 
-## v1.1.0 - 2020/10/06
+## v1.1.0 - White Elephant [2020-10-06]
 
 ### `Added`
 
@@ -826,7 +827,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - [#29](https://github.com/nf-core/mag/pull/29) - Change depreciated parameters: `--singleEnd` -> `--single_end`, `--igenomesIgnore` -> `--igenomes_ignore`
 
-## v1.0.0 - 2019/12/20
+## v1.0.0 - Purple Corgi [2019-12-20]
 
 Initial release of nf-core/mag, created with the [nf-core](http://nf-co.re/) template.
 

assets/multiqc_config.yml

@@ -1,5 +1,5 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/mag/tree/dev" target="_blank">nf-core/mag</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://nf-co.re/mag/dev/docs/output" target="_blank">documentation</a>.
+  This report has been generated by the <a href="https://github.com/nf-core/mag/releases/tag/5.2.0" target="_blank">nf-core/mag</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://nf-co.re/mag/5.2.0/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-mag-methods-description":
     order: -1000

nextflow.config

@@ -511,7 +511,7 @@ manifest {
     mainScript      = 'main.nf'
     defaultBranch   = 'main'
     nextflowVersion = '!>=25.04.2'
-    version         = '5.2.0dev'
+    version         = '5.2.0'
     doi             = '10.1093/nargab/lqac007'
 }