docs: document QC optimization changes for v4.0

Add comprehensive documentation for the performance-optimized QC defaults:

- Add "Quality Control Configuration" section to usage.md explaining the v4.0 changes
- Document which QC steps are now disabled by default and why
- Provide clear commands to restore comprehensive QC when needed
- Add guidance on when to enable extended QC analysis
- Update all affected QC sections in output.md with proper admonition notes
- Use consistent :::note syntax following nf-core documentation standards

Updates changelog with breaking changes and performance improvements.
Helps users understand the new defaults and migrate their workflows appropriately.

🤖 Generated with [Claude Code](https://claude.ai/code)

Co-Authored-By: Claude <[email protected]>

Author: edmundmiller

CHANGELOG.md

@@ -14,6 +14,9 @@ Special thanks to the following for their contributions to the release:
 ### Enhancements & fixes
 
 - [PR #1597](https://github.com/nf-core/rnaseq/pull/1597) - Bump version after release 3.20.0
+- **BREAKING:** Optimize default QC steps for performance - `skip_dupradar`, `skip_qualimap`, `skip_rseqc`, `skip_stringtie`, and `skip_bigwig` now default to `true` to improve pipeline runtime and reduce compute costs. Use `--skip_[tool] false` to restore previous behavior
+- Optimize RSEM performance for Fusion filesystem by using local temporary storage and scratch directive
+- Add fast mode optimization to dupRadar module for improved performance
 
 ## [[3.20.0](https://github.com/nf-core/rnaseq/releases/tag/3.20.0)] - 2025-08-18
 

docs/output.md

@@ -381,6 +381,10 @@ Unless you are using [UMIs](https://emea.illumina.com/science/sequencing-method-
 
 ### StringTie
 
+:::note
+StringTie is disabled by default starting in v4.0 to improve pipeline performance. Enable with `--skip_stringtie false`.
+:::
+
 <details markdown="1">
 <summary>Output files</summary>
 
@@ -396,6 +400,10 @@ Unless you are using [UMIs](https://emea.illumina.com/science/sequencing-method-
 
 ### BEDTools and bedGraphToBigWig
 
+:::note
+BigWig generation is disabled by default starting in v4.0 to reduce output file sizes and improve performance. Enable with `--skip_bigwig false`.
+:::
+
 <details markdown="1">
 <summary>Output files</summary>
 
@@ -411,6 +419,10 @@ The [bigWig](https://genome.ucsc.edu/goldenpath/help/bigWig.html) format is an i
 
 ### RSeQC
 
+:::note
+RSeQC analysis is disabled by default starting in v4.0 to improve pipeline performance. Enable with `--skip_rseqc false`.
+:::
+
 [RSeQC](<(http://rseqc.sourceforge.net/)>) is a package of scripts designed to evaluate the quality of RNA-seq data. This pipeline runs several, but not all RSeQC scripts. You can tweak the supported scripts you would like to run by adjusting the `--rseqc_modules` parameter which by default will run all of the following: `bam_stat.py`, `inner_distance.py`, `infer_experiment.py`, `junction_annotation.py`, `junction_saturation.py`,`read_distribution.py` and `read_duplication.py`.
 
 The majority of RSeQC scripts generate output files which can be plotted and summarised in the MultiQC report.
@@ -591,6 +603,10 @@ RSeQC documentation: [tin.py](http://rseqc.sourceforge.net/#tin-py)
 
 ### Qualimap
 
+:::note
+Qualimap analysis is disabled by default starting in v4.0 due to its resource-intensive nature. Enable with `--skip_qualimap false`.
+:::
+
 <details markdown="1">
 <summary>Output files</summary>
 
@@ -616,6 +632,10 @@ The [Qualimap RNA-seq QC module](http://qualimap.bioinfo.cipf.es/doc_html/analys
 
 ### dupRadar
 
+:::note
+dupRadar analysis is disabled by default starting in v4.0 as it provides limited utility for bulk RNA-seq experiments. Enable with `--skip_dupradar false`.
+:::
+
 <details markdown="1">
 <summary>Output files</summary>
 

docs/usage.md

@@ -46,16 +46,19 @@ If you set the strandedness value to `auto`, the pipeline will sub-sample the in
 #### Usage Examples
 
 1. **Forward Stranded Sample:**
+
    - Forward fraction: 0.85
    - Reverse fraction: 0.15
    - **Classification:** Forward stranded
 
 2. **Reverse Stranded Sample:**
+
    - Forward fraction: 0.1
    - Reverse fraction: 0.9
    - **Classification:** Reverse stranded
 
 3. **Unstranded Sample:**
+
    - Forward fraction: 0.45
    - Reverse fraction: 0.55
    - **Classification:** Unstranded
@@ -139,6 +142,54 @@ You can use `--skip_alignment --skip_pseudo_alignment` if you only want to run t
 
 Note that `--skip_alignment` and `--skip_pseudo_alignment` prevent both the execution of alignment/pseudoalignment steps and the building of their corresponding indices. For example, using `--skip_alignment` with `--aligner star_salmon` will skip both STAR alignment and index building.
 
+## Quality Control Configuration
+
+### Performance-Optimized Defaults (v4.0+)
+
+Starting in version 4.0, several QC steps are disabled by default to improve pipeline performance and reduce compute costs for typical bulk RNA-seq analysis:
+
+- **`--skip_dupradar true`** - Disable dupRadar analysis (limited utility for bulk RNA-seq experiments)
+- **`--skip_qualimap true`** - Disable Qualimap alignment QC (resource-intensive step)
+- **`--skip_rseqc true`** - Disable RSeQC analysis suite (7 comprehensive RNA-seq modules)
+- **`--skip_stringtie true`** - Disable StringTie transcriptome assembly (additional processing overhead)
+- **`--skip_bigwig true`** - Disable BigWig coverage track generation (large output files)
+
+These changes can significantly reduce pipeline runtime and computational requirements while preserving essential QC metrics through FastQC, MultiQC, and basic alignment statistics.
+
+### Enabling Comprehensive QC
+
+For detailed quality control analysis, you can re-enable any or all QC steps:
+
+```bash
+# Enable all QC steps (restore pre-v4.0 behavior)
+nextflow run nf-core/rnaseq \
+  --skip_dupradar false \
+  --skip_qualimap false \
+  --skip_rseqc false \
+  --skip_stringtie false \
+  --skip_bigwig false
+
+# Enable specific QC modules only
+nextflow run nf-core/rnaseq --skip_qualimap false --skip_rseqc false
+
+# Use the master QC toggle to enable most QC steps
+nextflow run nf-core/rnaseq --skip_qc false
+```
+
+### When to Enable Extended QC
+
+Consider enabling additional QC steps when:
+
+- Working with novel samples, non-standard protocols, or unusual experimental designs
+- Troubleshooting alignment, quantification, or data quality issues
+- Publishing datasets that require comprehensive QC documentation
+- Optimizing library preparation or sequencing protocols
+- Performing method comparisons or validation studies
+
+:::note
+Essential QC steps like FastQC, MultiQC, and alignment metrics remain enabled by default and provide sufficient quality assessment for most RNA-seq analyses.
+:::
+
 ### Sentieon acceleration for STAR
 
 The STAR aligner can be accelerated through its Sentieon implemention using the parameter `--use_sentieon_star`.