Merge branch 'refactor/split-prepare-genome' of github.com:nf-core/rnaseq into refactor/split-prepare-genome

Author: pinin4fjords

.nf-core.yml

@@ -3,7 +3,6 @@ lint:
   container_configs: false
   files_exist:
     - conf/modules.config
-    - assets/multiqc_config.yml
     - conf/containers_conda_lock_files_amd64.config
     - conf/containers_conda_lock_files_arm64.config
     - conf/containers_docker_amd64.config
@@ -20,7 +19,6 @@ lint:
     - .gitignore
     - nf-test.config
   modules_config: false
-  multiqc_config: false
   nextflow_config:
     - config_defaults:
         - params.ribo_database_manifest

CHANGELOG.md

@@ -14,6 +14,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [PR #1849](https://github.com/nf-core/rnaseq/pull/1849) - Tidy-up batch addressing [#1845](https://github.com/nf-core/rnaseq/issues/1845): README/schema clarifications, `&` → `&&` in three guards, deduplicated `withName` blocks, and removal of the unmaintained `bin/fastq_dir_to_samplesheet.py` (use [nf-core/fetchngs](https://nf-co.re/fetchngs) for samplesheet generation)
 - [PR #1850](https://github.com/nf-core/rnaseq/pull/1850) - Use the active aligner's display name in the MultiQC `fail_mapped` per-sample status row, and drop the hardcoded "STAR" reference from the pipeline-completion `min_mapped_reads` warning, so Bowtie2 reports no longer mislabel the metric as STAR ([#1846](https://github.com/nf-core/rnaseq/issues/1846))
 - [PR #1851](https://github.com/nf-core/rnaseq/pull/1851) - Split `PREPARE_GENOME` into `PREPARE_GENOME_REFERENCES` (FASTA / GTF / BED / transcript FASTA / chrom.sizes / rRNA / Kraken DB) and `PREPARE_GENOME_INDICES` (per-aligner index build/load) for clearer ownership; no user-facing parameter, output, or behaviour change ([#1721](https://github.com/nf-core/rnaseq/issues/1721)).
+- [PR #1852](https://github.com/nf-core/rnaseq/pull/1852) - Flatten `workflows/rnaseq/assets/` back to top-level `assets/` so `nf-core pipelines bump-version` finds `assets/multiqc_config.yml` and updates the report-comment URLs automatically on release bumps
 
 ## [[3.26.0](https://github.com/nf-core/rnaseq/releases/tag/3.26.0)] - 2026-05-07
 

…naseq/assets/multiqc/biotypes_header.txt assets/biotypes_header.txtworkflows/rnaseq/assets/multiqc/biotypes_header.txt renamed to assets/biotypes_header.txt workflows/rnaseq/assets/multiqc/biotypes_header.txt renamed to assets/biotypes_header.txt

@@ -83,11 +83,11 @@ report_section_order:
   star_rsem_deseq2_clustering:
     order: 1000
   # Summaries
-  "nf-core-rnaseq-methods-description-module":
+  "nf-core-rnaseq-methods-description":
     order: -1000
-  "software_versions-module":
+  "software_versions":
     order: -1001
-  "nf-core-rnaseq-summary-module":
+  "nf-core-rnaseq-summary":
     order: -1002
 
 export_plots: true