Merge pull request #948 from nf-core/dev

Release: v5.3.0 Rainbow Rattlesnake

Author: dialvarezs

.github/workflows/awsfulltest.yml

@@ -37,7 +37,7 @@ jobs:
             }
           profiles: test_full
 
-      - uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
+      - uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
         with:
           name: Seqera Platform debug log file
           path: |

.github/workflows/awstest.yml

@@ -25,7 +25,7 @@ jobs:
             }
           profiles: test
 
-      - uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
+      - uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
         with:
           name: Seqera Platform debug log file
           path: |

.github/workflows/download_pipeline.yml

@@ -127,7 +127,7 @@ jobs:
           fi
 
       - name: Upload Nextflow logfile for debugging purposes
-        uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
+        uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
         with:
           name: nextflow_logfile.txt
           path: .nextflow.log*

.github/workflows/fix_linting.yml

@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       # Use the @nf-core-bot token to check out so we can push later
-      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 

.github/workflows/linting.yml

@@ -11,7 +11,7 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
 
       - name: Set up Python 3.14
         uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
@@ -28,7 +28,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+        uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v2
@@ -71,7 +71,7 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
+        uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
         with:
           name: linting-logs
           path: |

.github/workflows/nf-test.yml

@@ -40,7 +40,7 @@ jobs:
           rm -rf ./* || true
           rm -rf ./.??* || true
           ls -la ./
-      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
         with:
           fetch-depth: 0
 
@@ -86,7 +86,7 @@ jobs:
       TOTAL_SHARDS: ${{ needs.nf-test-changes.outputs.total_shards }}
 
     steps:
-      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
         with:
           fetch-depth: 0
 

.github/workflows/template-version-comment.yml

@@ -9,7 +9,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+        uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
         with:
           ref: ${{ github.event.pull_request.head.sha }}
 

.nf-core.yml

@@ -6,7 +6,7 @@ lint:
     - config_defaults:
         - params.phix_reference
         - params.lambda_reference
-nf_core_version: 3.4.1
+nf_core_version: 3.5.1
 repository_type: pipeline
 template:
   author: "Hadrien Gourlé, Daniel Straub, Sabrina Krakau, James A. Fellows Yates, Maxime Borry"
@@ -16,4 +16,4 @@ template:
   name: mag
   org: nf-core
   outdir: .
-  version: 5.2.0
+  version: 5.3.0

.prettierignore

@@ -12,3 +12,5 @@ testing*
 bin/
 .nf-test/
 ro-crate-metadata.json
+modules/nf-core/
+subworkflows/nf-core/

CHANGELOG.md

@@ -3,6 +3,51 @@
 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).
 
+## v5.3.0 - Rainbow Rattlesnake [2025-12-05]
+
+### `Added`
+
+- [#905](https://github.com/nf-core/mag/pull/905) - Add nf-test snapshot for `test_assembly_input` profile (by @dialvarezs)
+- [#930](https://github.com/nf-core/mag/pull/930) - Add binner SemiBin2 (by @d4straub)
+- [#861](https://github.com/nf-core/mag/pull/861) - Added `--generate_bigmag_file` to execute the bigmag workflow that generates the file to be used as input for [BIgMAG](https://github.com/jeffe107/BIgMAG) (added by @jeffe107)
+
+### `Changed`
+
+- [#932](https://github.com/nf-core/mag/pull/932) - Replaced usages of deprecated `Channel()` with `channel()` and fix other LSP warnings (by @dialvarezs)
+- [#937](https://github.com/nf-core/mag/pull/937) - Updated to nf-core 3.5.1 `TEMPLATE` (by @dialvarezs)
+- [#938](https://github.com/nf-core/mag/pull/938) - Update nf-core modules (by @dialvarezs)
+
+### `Fixed`
+
+- [#894](https://github.com/nf-core/mag/pull/894) - Fix read order in metaSPAdes to allow co-assembly of paired-end data of multiple samples (reported by @maartenciers, fix by @jfy133 with contributions from @prototaxites, @d4straub and @dialvarezs)
+- [#927](https://github.com/nf-core/mag/pull/927) - MetaBinner now succeeds when no contigs are too short or all are binned (reported by @MicroSeq, fix by @d4straub)
+- [#929](https://github.com/nf-core/mag/pull/929) - Allow the domain_classification.R script to run with any assembler, not just Megahit or Spades (reported by @MicroSeq, fix by @prototaxites)
+- [#943](https://github.com/nf-core/mag/pull/943) - Fixed concatenation of BUSCO summaries with uneven columns by changing from `csvtk` to `qsv` (reported by @jfy133 and @julianu, fix by @dialvarezs)
+- [#943](https://github.com/nf-core/mag/pull/943) - Fixed creation of the Tiara report channel used for concatenation (by @dialvarezs)
+- [#945](https://github.com/nf-core/mag/pull/945) - Skip mixing of GTDB-Tk MultiQC files when binning is skipped (reported by @amizeranschi, fix by @dialvarezs)
+- [#953](https://github.com/nf-core/mag/pull/953) - metaSPAdes retries upon error 250 (out of memory), rather than finishing the pipeline.
+- [#954](https://github.com/nf-core/mag/pull/954) - Skip GTDB-Tk when no bin QC tool is enabled and add warning messages (fix by @dialvarezs)
+- [#956](https://github.com/nf-core/mag/pull/956) - Support long reads assemblers in assembly input (fix by @dialvarezs)
+
+### `Dependencies`
+
+| Tool     | Previous version | New version |
+| -------- | ---------------- | ----------- |
+| bcftools | 1.21             | 1.22        |
+| csvtk    | 0.31.0           |             |
+| fastp    | 0.24.0           | 1.0.1       |
+| geNomad  | 1.11.1           | 1.11.2      |
+| metamdbg | 1.1              | 1.2         |
+| mmseqs   | 17.b804f         | 18.8cc5c    |
+| nf-core  |                  | 3.5.1       |
+| qsv      |                  | 5.1.0       |
+| samtools | 1.21             | 1.22.1      |
+| SemiBin2 |                  | 2.2.0       |
+
+### `Deprecated`
+
+- [#943](https://github.com/nf-core/mag/pull/943) - Remove `csvtk/concat` module (by @dialvarezs).
+
 ## v5.2.0 - Puce Pangolin [2025-11-07]
 
 ### `Added`