Merge pull request #1849 from nf-core/tidy-up-1845

Tidy-up batch: docs, schema, configs, single trivial correctness fix

Author: pinin4fjords

CHANGELOG.md

@@ -11,6 +11,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - [PR #1844](https://github.com/nf-core/rnaseq/pull/1844) - Bump version to 3.27.0dev after release 3.26.0; flip the MultiQC report links and RO-Crate URL/version back to dev
 - [PR #1848](https://github.com/nf-core/rnaseq/pull/1848) - Align `actions/checkout` SHA in `nf-test-arm.yml` and `nf-test-gpu.yml` with the template-derived `nf-test.yml` (`v6`) ([#1847](https://github.com/nf-core/rnaseq/issues/1847))
+- [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)
 
 ## [[3.26.0](https://github.com/nf-core/rnaseq/releases/tag/3.26.0)] - 2026-05-07
 

README.md

@@ -47,9 +47,10 @@
     1. [`RSeQC`](http://rseqc.sourceforge.net/)
     2. [`Qualimap`](http://qualimap.bioinfo.cipf.es/)
     3. [`dupRadar`](https://bioconductor.org/packages/release/bioc/html/dupRadar.html)
-    4. [`Preseq`](http://smithlabresearch.org/software/preseq/)
+    4. [`Preseq`](http://smithlabresearch.org/software/preseq/) (_disabled by default; enable with `--skip_preseq false`_)
     5. [`DESeq2`](https://bioconductor.org/packages/release/bioc/html/DESeq2.html)
-    6. Contamination detection on selected screening reads (unaligned by default); _optional_
+    6. Or, _experimental_: [`RustQC`](https://github.com/seqeralabs/rustqc) as a single-pass alternative to RSeQC, Qualimap, dupRadar, Preseq, and SAMtools stats (enable with `--use_rustqc`; recommend trialling on pilot data first).
+    7. Contamination detection on selected screening reads (unaligned by default); _optional_
        1. [`Kraken2`](https://ccb.jhu.edu/software/kraken2/) -> [`Bracken`](https://ccb.jhu.edu/software/bracken/)
        2. [`Sylph`](https://sylph-docs.github.io/)
 15. Pseudoalignment and quantification ([`Salmon`](https://combine-lab.github.io/salmon/) or ['Kallisto'](https://pachterlab.github.io/kallisto/); _optional_)

bin/fastq_dir_to_samplesheet.py

@@ -135,9 +135,6 @@ process {
 
             args.join(' ')
         }
-    }
-
-    withName: '.*ALIGN_STAR:STAR_ALIGN|.*ALIGN_STAR:SENTIEON_STAR_ALIGN|.*ALIGN_STAR:PARABRICKS_RNA_FQ2BAM' {
         publishDir = [
             [
                 path: { "${params.outdir}/${task.ext.publish_prefix}${params.aligner}/log" },

conf/modules/align_star.config

@@ -10,12 +10,4 @@ process {
             mode: params.publish_dir_mode
         ]
     }
-
-    withName: 'CUSTOM_MULTIQCCUSTOMBIOTYPE' {
-        publishDir = [
-            path: { "${params.outdir}/${task.ext.publish_prefix}${params.aligner}/featurecounts" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
 }

conf/modules/featurecounts.config

@@ -72,6 +72,8 @@ process DESEQ2_QC {
 
     mkdir size_factors
     touch size_factors/${prefix}.size_factors.RData
+    # One per-sample size_factors file per data column in $counts; the
+    # module test snaps these names so the stub must mirror real-run output.
     for i in `head $counts -n 1 | cut -f3-`;
     do
         touch size_factors/\${i}.size_factors.RData

modules/local/deseq2_qc/main.nf

@@ -550,13 +550,13 @@
                 },
                 "kallisto_quant_fraglen": {
                     "type": "integer",
-                    "description": "In single-end mode Kallisto requires an estimated fragment length. Specify a default value for that here. TODO: use existing RSeQC results to do this dynamically.",
+                    "description": "In single-end mode Kallisto requires an estimated fragment length (in base pairs). Specify a default value for that here.",
                     "default": 200,
                     "fa_icon": "fas fa-ruler-horizontal"
                 },
                 "kallisto_quant_fraglen_sd": {
                     "type": "integer",
-                    "description": "In single-end mode, Kallisto requires an estimated standard error for fragment length. Specify a default value for that here. TODO: use existing RSeQC results to do this dynamically.",
+                    "description": "In single-end mode, Kallisto requires an estimated standard error for fragment length (in base pairs). Specify a default value for that here.",
                     "default": 200,
                     "fa_icon": "fas fa-sort-amount-up-alt"
                 },
@@ -802,26 +802,31 @@
                 },
                 "skip_dupradar": {
                     "type": "boolean",
+                    "default": false,
                     "fa_icon": "fas fa-fast-forward",
-                    "description": "Skip dupRadar."
+                    "description": "Skip dupRadar. Has no effect under `--use_rustqc` (experimental)."
                 },
                 "skip_qualimap": {
                     "type": "boolean",
+                    "default": false,
                     "fa_icon": "fas fa-fast-forward",
-                    "description": "Skip Qualimap."
+                    "description": "Skip Qualimap. Has no effect under `--use_rustqc` (experimental)."
                 },
                 "skip_rseqc": {
                     "type": "boolean",
+                    "default": false,
                     "fa_icon": "fas fa-fast-forward",
-                    "description": "Skip RSeQC."
+                    "description": "Skip RSeQC. Has no effect under `--use_rustqc` (experimental)."
                 },
                 "skip_biotype_qc": {
                     "type": "boolean",
+                    "default": false,
                     "fa_icon": "fas fa-fast-forward",
-                    "description": "Skip additional featureCounts process for biotype QC."
+                    "description": "Skip additional featureCounts process for biotype QC. Has no effect under `--use_rustqc` (experimental)."
                 },
                 "skip_deseq2_qc": {
                     "type": "boolean",
+                    "default": false,
                     "fa_icon": "fas fa-fast-forward",
                     "description": "Skip DESeq2 PCA and heatmap plotting."
                 },