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RustQC testing#1

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ewels wants to merge 15 commits intodev from
rustqc
Open

RustQC testing #1
ewels wants to merge 15 commits intodev from
rustqc

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@ewels ewels commented Feb 13, 2026

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github-actions bot commented Feb 13, 2026 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 9c183e5 

+| ✅ 204 tests passed |+
#| ❔ 9 tests were ignored |#
!| ❗ 8 tests had warnings |!
Details

❗ Test warnings:

  • files_exist - File not found: assets/multiqc_config.yml
  • pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.5.1
  • Run at 2026年02月16日 16:30:39

ewels added 14 commits February 13, 2026 18:32 
Integrate all 7 RSeQC tools (bam_stat, infer_experiment, read_duplication,
read_distribution, junction_annotation, junction_saturation, inner_distance)
into the single rustqc rna command. When RustQC is enabled, BAM_RSEQC only
runs for tin (which RustQC does not implement). Strandedness comparison uses
infer_experiment output from whichever tool produces it.
Upstream RustQC now derives transcript structure directly from GTF,
making --gtf and --bed mutually exclusive. With --gtf, all analyses
(dupRadar, featureCounts, and RSeQC tools) run without a BED file.
BED file flow is retained for BAM_RSEQC (tin module).
- Add --flat-output flag since RustQC now writes to subfolders by default
- Add SVG output declarations for all plot outputs (PNG + SVG pairs)
- Rename plot emit names with _png/_svg suffixes for clarity
- Update publishDir patterns to include SVG files
- Update stub section with SVG files
- Add TIN, preseq, samtools flagstat/idxstats/stats, and Qualimap gene
 body coverage outputs to the RustQC module and publishDir config
- Rename --skip_rustqc (default true) to --use_rustqc (default false)
 as a single toggle that automatically disables all replaced tools
- When --use_rustqc is enabled, dupRadar, featureCounts biotype QC,
 RSeQC, Preseq, Qualimap, and samtools stats are all skipped
- Wire all new RustQC outputs to MultiQC
... enabled
Use ext.when config to skip BAM_STATS_SAMTOOLS processes inside
BAM_MARKDUPLICATES_PICARD and BAM_SORT_STATS_SAMTOOLS subworkflows
when RustQC provides equivalent outputs.
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