chore(pridepy): bump to 0.0.15 & feat(qpx): add QPX export module

[Shen-YuFei]

Description

1. chore(pridepy): Bump pridepy container from 0.0.14 to 0.0.15.
   BioContainers image quay.io/biocontainers/pridepy:0.0.15--pyhdfd78af_0 is already available.

2. feat(qpx): Add QPX Parquet + MuData export module.

   • main.nf: QPX_EXPORT process converts DIA-NN output to QPX Parquet dataset and MuData .h5mu
   • meta.yml, environment.yml: module metadata and dependencies
   • tests/: nf-test stub test with snapshot assertion
   • Container: ghcr.io/bigbio/qpx:<qpx_version>

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)

Module Type

• New module
• Module update

[qodo-code-review]

ⓘ You've reached your Qodo monthly free-tier limit. Reviews pause until next month — upgrade your plan to continue now, or link your paid account if you already have one.

[coderabbitai]

Important

Review skipped

Auto reviews are disabled on base/target branches other than the default branch.

Please check the settings in the CodeRabbit UI or the .coderabbit.yaml file in this repository. To trigger a single review, invoke the @coderabbitai review command.

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro

Run ID: 171985e2-70d5-4638-b26f-58a9031b93c2

You can disable this status message by setting the reviews.review_status to false in the CodeRabbit configuration file.

Use the checkbox below for a quick retry:

• 🔍 Trigger review

✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests

Tip

💬 Introducing Slack Agent: The best way for teams to turn conversations into code.

Slack Agent is built on CodeRabbit's deep understanding of your code, so your team can collaborate across the entire SDLC without losing context.

• Generate code and open pull requests
• Plan features and break down work
• Investigate incidents and troubleshoot customer tickets together
• Automate recurring tasks and respond to alerts with triggers
• Summarize progress and report instantly

Built for teams:

• Shared memory across your entire org—no repeating context
• Per-thread sandboxes to safely plan and execute work
• Governance built-in—scoped access, auditability, and budget controls

One agent for your entire SDLC. Right inside Slack.

👉 Get started

---

Thanks for using CodeRabbit! It's free for OSS, and your support helps us grow. If you like it, consider giving us a shout-out.

❤️ Share

• X
• Mastodon
• Reddit
• LinkedIn

_{Comment @coderabbitai help to get the list of available commands and usage tips.}

[codacy-production]

Up to standards ✅

🟢 Issues 0 issues

Results:
0 new issues

View in Codacy

_{NEW Get contextual insights on your PRs based on Codacy's metrics, along with PR and Jira context, without leaving GitHub. Enable AI reviewer
TIP This summary will be updated as you push new changes.}

[Copilot]

Pull request overview

Updates the bigbio/pridepy nf-core module to use pridepy 0.0.15, aligning the module’s container, conda environment, and test snapshots with the new upstream release.

Changes:

• Bump the PRIDEPY_DOWNLOAD process container tag from 0.0.14 to 0.0.15
• Update the conda dependency pin to bioconda::pridepy=0.0.15
• Refresh nf-test snapshot checksum(s) for versions.yml

Reviewed changes

Copilot reviewed 3 out of 3 changed files in this pull request and generated no comments.

File	Description
modules/bigbio/pridepy/main.nf	Updates container tag and stubbed versions output to 0.0.15
modules/bigbio/pridepy/environment.yml	Pins pridepy conda dependency to 0.0.15
modules/bigbio/pridepy/tests/main.nf.test.snap	Updates expected snapshot md5 for the new versions output

---

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.

[qodo-code-review]

ⓘ You've reached your Qodo monthly free-tier limit. Reviews pause until next month — upgrade your plan to continue now, or link your paid account if you already have one.