Move to thermorawfileparser to 2.0.0dev

[ypriverol]

Pull Request

Description

Checklist

• Module follows nf-core standards
• main.nf includes process definition
• meta.yml includes complete documentation
• environment.yml specifies dependencies
• Tests are included
• Code is formatted (prettier)
• CI checks pass

Module Type

• New module
• Module update
• Bug fix
• Documentation

Related Issues

Closes #

Summary by CodeRabbit

• Chores

  • Updated ThermoRawFileParser dependency to a newer development release.
  • Updated container image references used for execution across runtime modes.
  • Adjusted Nextflow-related ignore patterns to better control excluded artifacts.

• Tests

  • Switched test data endpoints to FTP-hosted PRIDE URLs for onsite proteomics fixtures.

[coderabbitai]

No actionable comments were generated in the recent review. 🎉

ℹ️ Recent review info

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro

Run ID: 4b444a2f-3b00-4e6a-8c8f-23258112794c

📥 Commits

Reviewing files that changed from the base of the PR and between bdaea6f and 169640e.

⛔ Files ignored due to path filters (2)

• modules/bigbio/onsite/tests/main.nf.test.snap is excluded by !**/*.snap
• modules/bigbio/thermorawfileparser/tests/main.nf.test.snap is excluded by !**/*.snap

📒 Files selected for processing (1)

• .gitignore

🚧 Files skipped from review as they are similar to previous changes (1)

• .gitignore

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📝 Walkthrough

Walkthrough

Bumped ThermoRawFileParser from 1.4.5 to 2.0.0.dev in the Conda environment; updated Nextflow process image tags and executable/version checks from ThermoRawFileParser.sh to thermorawfileparser; switched test-data URLs to PRIDE FTP; added .nf-test* ignore patterns.

Changes

Cohort / File(s)	Summary
ThermoRawFileParser module modules/bigbio/thermorawfileparser/environment.yml, modules/bigbio/thermorawfileparser/main.nf	Updated Conda package pin from 1.4.5 → 2.0.0.dev; replaced container image tags; changed command and version checks from ThermoRawFileParser.sh → thermorawfileparser.
Test data config tests/config/test_data.config	Replaced GitHub-hosted test data URLs with PRIDE FTP endpoints for onsite proteomics mzML and idXML test files.
Repository ignores .gitignore	Adjusted Nextflow ignore patterns: removed leading-dot rule for nf.test.snap and added .nf-test* pattern to ignore additional Nextflow test artifacts.

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~10 minutes

Possibly related PRs

• 🚧 update thermorawfileparser #26: Modifies the thermorawfileparser module and overlaps on version/container references.
• First iteration for thermorawfileparser #2: Updates thermorawfileparser invocation and package/image version (directly related).

Suggested labels

Review effort 2/5

Suggested reviewers

• daichengxin

Poem

🐰 I hopped through configs, light and spry,
Bumped a parser, gave it wings to fly,
FTP crumbs for tests I found,
Ignored small traces on the ground,
A tiny patch — a joyful cry!

🚥 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 'Move to thermorawfileparser to 2.0.0dev' directly and clearly summarizes the main change: upgrading the thermorawfileparser dependency from version 1.4.5 to 2.0.0.dev across environment.yml and main.nf files.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.

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✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch dev

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