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Update tower yml reports#762

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pinin4fjords merged 7 commits intodevfrom
update-tower-yml-reports
Sep 5, 2025
Merged

Update tower yml reports#762
pinin4fjords merged 7 commits intodevfrom
update-tower-yml-reports

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@pinin4fjords pinin4fjords commented Sep 5, 2025

Summary

I reviewed the S3 output directory and found several PDF and HTML reports that weren't being captured by the current tower.yml configuration. This PR adds the missing patterns to ensure all generated reports are displayed in Platform.

What I found

Missing HTML reports:

  • FastQC reports (*_fastqc.html)
  • FusionInspector web interface (*.fusion_inspector_web.html)
  • Individual fusion report HTML files (16 gene-specific reports like AKAP9_BRAF.html, EML4_ALK.html, etc.)
  • Pipeline execution and DAG reports

Changes

  • Added 5 new HTML report patterns
  • Fixed VCF pattern to match actual file extensions (.vcf instead of .vcf.gz)

PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/rnafusion branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

@pinin4fjords
feat: add missing PDF and HTML report patterns to tower.yml
3901adb 
- Add FastQC HTML reports for both original and trimmed reads
- Add FusionInspector web HTML report pattern
- Add individual fusion report HTML files from fusionreport
- Add MultiQC HTML report and PDF plots patterns
- Add pipeline execution and DAG HTML reports
- Update Picard PDF pattern to be more general
- Fix VCF pattern to match actual file extensions

These changes ensure all PDF and HTML files generated by the pipeline
are properly captured in Tower's report visualization system.
@pinin4fjords
Remove MultiQC PDF plots pattern
49c4231 
Individual PDF plots are not useful as standalone reports in Tower.
@pinin4fjords
Remove duplicate MultiQC report pattern
7dfe4eb 
The original multiqc_report.html pattern already covers this file.
@pinin4fjords
Remove redundant fusionreport index pattern
44e9277 
The broader fusionreport/*/*.html pattern already covers the index file.
@pinin4fjords
Add missing PDF and HTML report patterns to tower.yml
fc01d42 
- Add FastQC HTML reports for original and trimmed reads
- Add FusionInspector web HTML report
- Add individual fusion report HTML files
- Add pipeline execution and DAG HTML reports
- Update Picard PDF pattern to be more general
- Fix VCF pattern to match actual file extensions
@pinin4fjords
Revert Picard PDF display name change
b1c98ff 
Keep original display name for existing pattern.
@pinin4fjords
Revert unnecessary Picard PDF pattern change
126c07e 
The original *pdf pattern already works fine for matching .pdf files.
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github-actions bot commented Sep 5, 2025 •
edited
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 126c07e

+| ✅ 304 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   8 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 nextflow.config: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0
  • schema_lint - Input mimetype is missing or empty
  • schema_description - No description provided in schema for parameter: save_trimmed_fail
  • schema_description - No description provided in schema for parameter: min_trimmed_reads
  • schema_description - No description provided in schema for parameter: save_merged

❔ Tests ignored:

  • files_exist - File is ignored: tests/default.nf.test
  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md

✅ Tests passed:

Run details

  • nf-core/tools version 3.3.2
  • Run at 2025-09-05 11:21:08

@pinin4fjords pinin4fjords merged commit 74ac1f9 into dev Sep 5, 2025
8 checks passed
@pinin4fjords pinin4fjords deleted the update-tower-yml-reports branch September 5, 2025 13:11
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Reviewers

@FriederikeHanssen FriederikeHanssen FriederikeHanssen approved these changes

@rannick rannick rannick approved these changes

@nvnieuwk nvnieuwk Awaiting requested review from nvnieuwk nvnieuwk is a code owner

@atrigila atrigila Awaiting requested review from atrigila atrigila is a code owner

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3 participants

@pinin4fjords @FriederikeHanssen @rannick