Improvements for single cell proteomics DIANN

[ypriverol]

Pull Request

Description

Brief description of the changes made in this PR.

Type of Change

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to not work as expected)
• Documentation update
• Performance improvement
• Code refactoring
• Test addition/update
• Updates to the dependencies has been done.

Summary by CodeRabbit

• New Features

  • Added support for registering and analyzing single-cell DIA-NN datasets.

• Documentation

  • Added example reports and config entries showcasing single-cell DIA-NN workflows.

• Improvements

  • More accurate peptide and proteotypic handling in per-run statistics and visualizations.

• Chores

  • Added end-to-end automated testing and artifact upload for single-cell DIANN datasets.

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[coderabbitai]

Caution

Review failed

The pull request is closed.

📝 Walkthrough

Walkthrough

Adds a new GitHub Actions job to test single-cell DIANN datasets, two docs/config entries for PXD053464, and refactors DIA utility peptide handling to use Modified.Sequence and Proteotypic fields.

Changes

Cohort / File(s)	Summary
CI workflow /.github/workflows/python-app.yml	Adds test_single_cell_diann job: checks out code, sets up Python 3.10, installs package, downloads/unzips PXD053464 DIANN bundle, runs MultiQC with DIANN plugin, uploads results_single_cell_diann artifact.
Documentation & config docs/README.md, docs/config.json	Adds two example report rows for "Single cell (DIA-NN)" and two docs/config.json project entries (PXD053464 and PXD053464_disable_hoverinfo) pointing to the same ZIP URL and file_type metadata.
DIA utilities refactor pmultiqc/modules/common/dia_utils.py	Replaces internal sequence field usage with Modified.Sequence for peptide IDs, uses Proteotypic to determine unique peptides (with warning fallback), updates peptide/protein mapping and per-run statistics accordingly.

Sequence Diagram(s)

(omitted)

Estimated code review effort

🎯 4 (Complex) | ⏱️ ~45 minutes

Possibly related PRs

• Improvements for single cell proteomics DIANN  #593 — Similar edits: CI job addition, docs/config entries, and identical dia_utils refactor.
• Added the examples for DIANN #173 — Adds DIANN test job and config entries; overlaps CI and docs changes.

Suggested labels

Review effort 4/5

Suggested reviewers

• yueqixuan

Poem

🐰 Hopping through code with glee,
Single cells hum in harmony.
Proteotypic hops, sequences sing,
Tests and docs — a joyous spring.
Zip, unzip, report — carrots for me! 🥕

🚥 Pre-merge checks | ✅ 3

✅ Passed checks (3 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title 'Improvements for single cell proteomics DIANN' directly relates to the main changes across the PR, which add comprehensive support for single-cell DIANN datasets including workflow jobs, documentation, configuration entries, and utility updates.
Docstring Coverage	✅ Passed	Docstring coverage is 100.00% which is sufficient. The required threshold is 80.00%.

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✨ Finishing touches

• 📝 Generate docstrings

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[coderabbitai]

Actionable comments posted: 1

🤖 Fix all issues with AI agents

In `@pmultiqc/modules/common/dia_utils.py`:
- Around line 229-231: The selection of "Proteotypic" into report_data is
unguarded and will KeyError if the column is missing; update the code around
report_data (where df is filtered) to check for "Proteotypic" in df.columns and
if absent add a default (e.g., a column indicating all entries are proteotypic
or a sensible default value) or filter accordingly, and emit a warning/log via
the module logger; ensure changes reference the existing df and report_data
variables so downstream code continues to work with the same schema.

🧹 Nitpick comments (1)

docs/README.md (1)

245-245: Consider linking directly to the single-cell ZIP for consistency.

Most rows point to an archive file for one-click download; this one links to a folder. Linking to 03_SingleCell_Searches.zip would align with the rest of the table.

✏️ Suggested update

-| Single cell (DIA-NN) | Single cell dataset | [Single cell Example](https://pmultiqc.quantms.org/PXD053464/multiqc_report.html) ([disable_hoverinfo](https://pmultiqc.quantms.org/PXD053464_disable_hoverinfo/multiqc_report.html)) | [PXD053464 folder](https://ftp.pride.ebi.ac.uk/pride/data/archive/2024/08/PXD053464/) |
+| Single cell (DIA-NN) | Single cell dataset | [Single cell Example](https://pmultiqc.quantms.org/PXD053464/multiqc_report.html) ([disable_hoverinfo](https://pmultiqc.quantms.org/PXD053464_disable_hoverinfo/multiqc_report.html)) | [03_SingleCell_Searches.zip](https://ftp.pride.ebi.ac.uk/pride/data/archive/2024/08/PXD053464/03_SingleCell_Searches.zip) |