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[Fix] Summarize: wide format#311

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jonasscheid merged 5 commits intodevfrom
summarize-fix
Nov 10, 2025
Merged

[Fix] Summarize: wide format#311
jonasscheid merged 5 commits intodevfrom
summarize-fix

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@axelwalter
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@axelwalter axelwalter commented Nov 6, 2025

Construction of the wide summary dataframe would fail in some files due to MulitIndex issues in

  `summary_binder = best.groupby(peptide_col)['binder'].any().reset_index()`

Use nsmallest/nlargest in _pick_best instead of idxmin/idxmax to ensure
DataFrame with single-index as return type to avoid MultiIndex issues.

Also updated the conda environment.yml file for summarize results to install the mhcgnomes package (contains every requirement such as pandas).

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/epitopeprediction branch on the nf-core/test-datasets repository.
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github-actions Bot commented Nov 6, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 25bc070

+| ✅ 235 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   3 tests had warnings |!
Details

❗ Test warnings:

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: assets/nf-core-epitopeprediction_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-epitopeprediction_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-epitopeprediction_logo_dark.png

✅ Tests passed:

Run details

  • nf-core/tools version 3.4.1
  • Run at 2025-11-10 08:34:44

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jonasscheid commented Nov 7, 2025

@nf-core-bot fix linting

jonasscheid
jonasscheid requested changes Nov 7, 2025
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Comment thread bin/summarize_results.py
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jonasscheid
jonasscheid approved these changes Nov 10, 2025
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LGTM, thanks!!

@jonasscheid jonasscheid merged commit 373ee58 into dev Nov 10, 2025
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@jonasscheid jonasscheid deleted the summarize-fix branch March 4, 2026 10:30
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@jonasscheid jonasscheid jonasscheid approved these changes

@christopher-mohr christopher-mohr Awaiting requested review from christopher-mohr christopher-mohr is a code owner

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