Merge pull request #914 from nf-core/dev

 Release: v5.2.0 Puce Pangolin

Author: dialvarezs

.github/workflows/nf-test.yml

@@ -64,7 +64,7 @@ jobs:
     runs-on: # use self-hosted runners
       - runs-on=${{ github.run_id }}-nf-test
       - runner=4cpu-linux-x64
-      - disk=large
+      - volume=80gb
     strategy:
       fail-fast: false
       matrix:

.github/workflows/release-announcements.yml

@@ -17,8 +17,7 @@ jobs:
       - name: get description
         id: get_description
         run: |
-          echo "description=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .description' >> $GITHUB_OUTPUT
-
+          echo "description=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .description')" >> $GITHUB_OUTPUT
       - uses: rzr/fediverse-action@master
         with:
           access-token: ${{ secrets.MASTODON_ACCESS_TOKEN }}
@@ -27,9 +26,7 @@ jobs:
           # https://docs.github.com/en/developers/webhooks-and-events/webhooks/webhook-events-and-payloads#release
           message: |
             Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
-
-            ${{ steps.get_topics.outputs.description }}
-
+            ${{ steps.get_description.outputs.description }}
             Please see the changelog: ${{ github.event.release.html_url }}
 
             ${{ steps.get_topics.outputs.topics }} #nfcore #openscience #nextflow #bioinformatics

.nf-core.yml

@@ -16,4 +16,4 @@ template:
   name: mag
   org: nf-core
   outdir: .
-  version: 5.1.0
+  version: 5.2.0

CHANGELOG.md

@@ -3,7 +3,38 @@
 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).
 
-## v5.1.0 - 2025-10-27
+## 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)
+- [#907](https://github.com/nf-core/mag/pull/907) - Include refined bins from all binners in the `DASTool/bins` output folder (by @AlexHoratio)
+- [#911](https://github.com/nf-core/mag/pull/911) - Ensure column order is consistent when generating depth summaries to prevent swapped results on merged depth summary (by @dialvarezs)
+- [#912](https://github.com/nf-core/mag/pull/912) - Fix validation of multiple sequencing platforms when using `binning_map_mode = "all"` (reported by @mjfi2sb3, fix by @dialvarezs)
+- [#921](https://github.com/nf-core/mag/pull/921) - Fix publishing of BUSCO files (reported by @joao1980, fix by @dialvarezs)
+
+### `Dependencies`
+
+| Tool       | Previous version | New version |
+| ---------- | ---------------- | ----------- |
+| MetaBinner |                  | 1.4.4-0     |
+
+### `Deprecated`
+
+- [#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`
 
@@ -30,7 +61,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Deprecated`
 
-## 5.0.0 - [2025-09-30]
+## v5.0.0 - Green Squirrel [2025-09-30]
 
 ### `Added`
 
@@ -102,7 +133,7 @@ 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`
 
@@ -138,7 +169,7 @@ 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`
 
@@ -187,7 +218,7 @@ 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`
 
@@ -222,7 +253,7 @@ 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`
 
@@ -236,7 +267,7 @@ 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`
 
@@ -268,7 +299,7 @@ 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`
 
@@ -296,7 +327,7 @@ 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`
 
@@ -315,7 +346,7 @@ 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`
 
@@ -338,7 +369,7 @@ 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`
 
@@ -358,7 +389,7 @@ 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`
 
@@ -379,7 +410,7 @@ 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`
 
@@ -396,7 +427,7 @@ 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`
 
@@ -412,7 +443,7 @@ 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`
 
@@ -437,7 +468,7 @@ 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`
 
@@ -459,7 +490,7 @@ 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`
 
@@ -484,7 +515,7 @@ 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`
 
@@ -548,7 +579,7 @@ 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`
 
@@ -585,7 +616,7 @@ 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`
 
@@ -598,7 +629,7 @@ 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`
 
@@ -631,7 +662,7 @@ 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`
 
@@ -654,7 +685,7 @@ 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`
 
@@ -670,7 +701,7 @@ 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`
 
@@ -705,7 +736,7 @@ 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`
 
@@ -725,7 +756,7 @@ 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`
 
@@ -735,7 +766,7 @@ 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`
 
@@ -752,7 +783,7 @@ 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`
 
@@ -797,7 +828,7 @@ 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.
 

CITATIONS.md

@@ -52,6 +52,10 @@
 
   > Alneberg, J., Bjarnason, B. S., de Bruijn, I., Schirmer, M., Quick, J., Ijaz, U. Z., Lahti, L., Loman, N. J., Andersson, A. F., & Quince, C. (2014). Binning metagenomic contigs by coverage and composition. Nature Methods, 11(11), 1144–1146. doi: 10.1038/nmeth.3103
 
+- [MetaBinner](https://doi.org/10.1186/s13059-022-02832-6)
+
+  > Wang Z, Huang P, You R, Sun F, Zhu S. MetaBinner: a high-performance and stand-alone ensemble binning method to recover individual genomes from complex microbial communities. Genome Biol. 2023 Jan 6;24(1):1. doi: 10.1186/s13059-022-02832-6. PMID: 36609515; PMCID: PMC9817263.
+
 - [DAS Tool](https://doi.org/10.1038/s41564-018-0171-1)
 
   > Sieber, C. M. K., et al. 2018. "Recovery of Genomes from Metagenomes via a Dereplication, Aggregation and Scoring Strategy." Nature Microbiology 3 (7): 836-43. doi: 10.1038/s41564-018-0171-1

README.md

@@ -47,7 +47,7 @@ The pipeline then:
 - performs assembly using [MEGAHIT](https://github.com/voutcn/megahit) and [SPAdes](http://cab.spbu.ru/software/spades/), and checks their quality using [Quast](http://quast.sourceforge.net/quast)
 - (optionally) performs ancient DNA assembly validation using [PyDamage](https://github.com/maxibor/pydamage) and contig consensus sequence recalling with [Freebayes](https://github.com/freebayes/freebayes) and [BCFtools](http://samtools.github.io/bcftools/bcftools.html)
 - predicts protein-coding genes for the assemblies using [Prodigal](https://github.com/hyattpd/Prodigal), and bins with [Prokka](https://github.com/tseemann/prokka) and optionally [MetaEuk](https://www.google.com/search?channel=fs&client=ubuntu-sn&q=MetaEuk)
-- performs metagenome binning using [MetaBAT2](https://bitbucket.org/berkeleylab/metabat/src/master/), [MaxBin2](https://sourceforge.net/projects/maxbin2/), [CONCOCT](https://github.com/BinPro/CONCOCT), and/or [COMEBin](https://github.com/ziyewang/COMEBin)
+- performs metagenome binning using [MetaBAT2](https://bitbucket.org/berkeleylab/metabat/src/master/), [MaxBin2](https://sourceforge.net/projects/maxbin2/), [CONCOCT](https://github.com/BinPro/CONCOCT), [COMEBin](https://github.com/ziyewang/COMEBin), and/or [MetaBinner](https://github.com/ziyewang/MetaBinner)
 - checks the quality of the genome bins using [Busco](https://busco.ezlab.org/), [CheckM](https://ecogenomics.github.io/CheckM/), or [CheckM2](https://github.com/chklovski/CheckM2) and optionally [GUNC](https://grp-bork.embl-community.io/gunc/)
 - Performs ancient DNA validation and repair with [pyDamage](https://github.com/maxibor/pydamage) and [freebayes](https://github.com/freebayes/freebayes)
 - optionally refines bins with [DAS Tool](https://github.com/cmks/DAS_Tool)
@@ -60,12 +60,6 @@ Furthermore, the pipeline creates various reports in the results directory speci
 > [!NOTE]
 > If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.
 
-```bash
-nextflow run nf-core/mag -profile <docker/singularity/podman/shifter/charliecloud/conda/institute> --input '*_R{1,2}.fastq.gz' --outdir <OUTDIR>
-```
-
-or
-
 ```bash
 nextflow run nf-core/mag -profile <docker/singularity/podman/shifter/charliecloud/conda/institute> --input samplesheet.csv --outdir <OUTDIR>
 ```
@@ -107,6 +101,7 @@ Other code contributors include:
 - [Nikolaos Vergoulidis](https://github.com/IceGreb)
 - [Greg Fedewa](https://github.com/harper357)
 - [Vini Salazar](https://github.com/vinisalazar)
+- [Alex Caswell](https://github.com/AlexHoratio)
 
 Long read processing was inspired by [caspargross/HybridAssembly](https://github.com/caspargross/HybridAssembly) written by Caspar Gross [@caspargross](https://github.com/caspargross)
 

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/releases/tag/5.1.0" 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/5.1.0/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