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Add --skip_qc_report parameter to skip Quarto report rendering#300

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nictru merged 1 commit into
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qc-report-cleanup
Jun 27, 2026
Merged

Add --skip_qc_report parameter to skip Quarto report rendering#300
nictru merged 1 commit into
devfrom
qc-report-cleanup

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@nictru

@nictru nictru commented Jun 27, 2026

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Summary

  • Add a --skip_qc_report pipeline parameter (default: false) to optionally skip rendering the Quarto QC HTML report in reports/.
  • Gate the QC_REPORT process in SCDOWNSTREAM so large runs can bypass the memory-heavy report step while keeping MultiQC and other pipeline outputs unchanged.

Test plan

  • Run the default test profile and confirm reports/qc-report.html is still produced
  • Re-run with --skip_qc_report and confirm the pipeline completes without reports/qc-report.html
  • Confirm MultiQC output is unchanged in both cases

@nictru
Add --skip_qc_report parameter to skip Quarto report rendering.
41e099b 
This lets large runs bypass the memory-heavy QC HTML report while keeping MultiQC and other pipeline outputs unchanged.
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github-actions Bot commented Jun 27, 2026

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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 41e099b

+| ✅ 298 tests passed       |+
#| ❔   1 tests had warnings |#
!| ❗  15 tests had warnings |!
Details

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • files_exist - File not found: conf/igenomes_ignored.config
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
  • pipeline_todos - TODO string in README.md: Add bibliography of tools and data used in your pipeline
  • pipeline_todos - TODO string in nextflow.config: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
  • 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!
  • pipeline_todos - TODO string in CONTRIBUTING.md: Add any pipeline specific contribution guidelines here, such as coding styles, procedures, checklists etc.
  • 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 nextflow.config: Specify any additional parameters here
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required

❔ Tests fixed:

✅ Tests passed:

Run details

  • nf-core/tools version 4.0.2
  • Run at 2026-06-27 13:42:40

@nictru nictru merged commit 61b838c into dev Jun 27, 2026
56 checks passed
@nictru nictru deleted the qc-report-cleanup branch June 27, 2026 14:47
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