Merge branch 'dev' into bwamem_fix

Author: eduard-watchmaker

.gitpod.yml

@@ -3,6 +3,9 @@ lint:
     - lib/nfcore_external_java_deps.jar
     - conf/modules.config
     - .github/workflows/ci.yml
+  files_unchanged:
+    - docs/images/nf-core-methylseq_logo_light.png
+    - docs/images/nf-core-methylseq_logo_dark.png
   modules_config: false
 nf_core_version: 3.5.1
 repository_type: pipeline

.nf-core.yml

@@ -3,14 +3,30 @@
 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).
 
-## [v4.2.0](https://github.com/nf-core/methylseq/releases/tag/4.2.0) - []
+## [v4.2.0](https://github.com/nf-core/methylseq/releases/tag/4.2.0) - [2025-12-05]
 
 ### Bug fixes & refactoring
 
+- 🐛 Fix error in `picard_bedtointervallist.config` [#566](https://github.com/nf-core/methylseq/pull/566)
+- 🔧 Update Bismark to v0.25.1 [#569](https://github.com/nf-core/methylseq/pull/569)
+- 🔧 Update MultiQC module
+
 ### Pipeline Updates
 
+- ✨ Added TAPS (TET-assisted pyridine borane sequencing) analysis workflow [#574](https://github.com/nf-core/methylseq/pull/574)
+  - Added rastair modules
+  - Removed methyldackel modules from fastq_align_dedup_bwameth subworkflow
+  - Added bam_methyldackel subworkflow which runs methyldackel modules
+  - Added fasta_index_methylseq subworkflow which indexes genomes for bismark, bwa-meth or bwa mem
+  - Added bam_taps_conversion to run rastair modules for TAPS data
+  - Added fastq_align_dedup_bwamem subworkflow to run bwa mem (+ gpu parabricks), dedup and run stats
+  - Updated bismark modules
+- 🔄 Updated template to nf-core/tools v3.5.1 [#577](https://github.com/nf-core/methylseq/pull/577)
+
 ### Testing Updates
 
+- 🧪 Updated nf-test GPU configuration
+
 ## [v4.1.0](https://github.com/nf-core/methylseq/releases/tag/4.1.0) - [2025-08-10]
 
 ### Bug fixes & refactoring

CHANGELOG.md

@@ -1,7 +1,7 @@
 <h1>
   <picture>
-    <source media="(prefers-color-scheme: dark)" srcset="docs/images/nf-core-methylseq_logo_dark.png">
-    <img alt="nf-core/methylseq" src="docs/images/nf-core-methylseq_logo_light.png">
+    <source media="(prefers-color-scheme: dark)" srcset="docs/images/nf-core-methylseq-dark.png">
+    <img alt="nf-core/methylseq" src="docs/images/nf-core-methylseq-light.png">
   </picture>
 </h1>
 
@@ -23,7 +23,7 @@
 
 **nf-core/methylseq** is a bioinformatics analysis pipeline used for Methylation (Bisulfite) sequencing data. It pre-processes raw data from FastQ inputs, aligns the reads and performs extensive quality-control on the results.
 
-![nf-core/methylseq metro map](docs/images/taps_metromap.png)
+![nf-core/methylseq metro map](docs/images/4.2.0_metromap.png)
 
 The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker / Singularity / Podman / Charliecloud / Apptainer containers making installation trivial and results highly reproducible.
 

README.md

@@ -1,5 +1,5 @@
-chr 150 200
-chr 2500    3000
-chr 5000    5418
-chr 20000   25000
-chr 35000   36000
+chr	150	200
+chr	2500	3000
+chr	5000	5418
+chr	20000	25000
+chr	35000	36000

assets/dummy_file.txt

@@ -1,7 +1,7 @@
 process {
     withName: RASTAIR_CALL {
         ext.args = [
-            // Pending the resolution of the mbias_parse process
+            // Pending the resolution of the mbiasparse process
             params.trim_OT ?: '0,0,10,0', // [r1_start, r1_end, r2_start, r2_end]
             params.trim_OB ?: '0,0,10,0' // [r1_start, r1_end, r2_start, r2_end]
         ].join(" ").trim()

assets/genome_target_regions.bed

@@ -1,4 +1,4 @@
 includeConfig "../modules/rastair_call.config"
 includeConfig "../modules/rastair_mbias.config"
-includeConfig "../modules/rastair_mbias_parser.config"
+includeConfig "../modules/rastair_mbiasparser.config"
 includeConfig "../modules/rastair_methylkit.config"