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Corrections to the CHANGELOG and report no longer reading the trace - #98

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MaximilianStammnitz merged 1 commit into
nf-core:devfrom
MaximilianStammnitz:dev
Nov 6, 2026
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Corrections to the CHANGELOG and report no longer reading the trace #98
MaximilianStammnitz merged 1 commit into
nf-core:devfrom
MaximilianStammnitz:dev

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@MaximilianStammnitz MaximilianStammnitz commented Nov 4, 2026 •
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Small fixes based on @maxulysse's review comments (#54)

Execution trace in the report

Until now, the report's "Run statistics" panel was built from Nextflow's execution trace, which the workflow read back from ${outdir}/pipeline_info/ while the run was still writing it. That breaks with remote outdirs, with user configs that switch the trace off or rename it, and with -resume. This PR:

  • workflows/deepmutscan.nf: no longer passes the trace to the report
  • build_summary_report.py: removes run_stats() and the trace input
  • summary_report_template.html: the "Run statistics" panel now links to Nextflow's execution report and timeline in pipeline_info/
  • docs/output.md, docs/usage.md: updated to match

CHANGELOG

PR checklist

  • This comment contains a description of changes (with reason).
  • Make sure your code lints (nf-core pipelines lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.

@MaximilianStammnitz
Correct --min_counts and add --output_pseudocount to the CHANGELOG; H…
3a459a7 
…TML report now links to Nextflow's execution report instead of reading the trace
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github-actions Bot commented Nov 4, 2026

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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 3a459a7

+| ✅ 243 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   2 tests had warnings |!
Details

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 1.0.0
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).

❔ Tests ignored:

  • files_exist - File is ignored: conf/igenomes.config
  • files_exist - File is ignored: conf/igenomes_ignored.config
  • files_unchanged - File ignored due to lint config: assets/nf-core-deepmutscan_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-deepmutscan_logo_dark.png

✅ Tests passed:

Run details

  • nf-core/tools version 4.2.1
  • Run at 2026-11-04 14:44:39

@MaximilianStammnitz
MaximilianStammnitz merged commit 04cb221 into nf-core:dev Nov 6, 2026
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@maxulysse maxulysse maxulysse approved these changes

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