feat!: download pangenome indexes from HPRC

[johanneskoester]

Building them on the fly from VCF is lossy (see here).

pangenome/release: 1.1 in combination with ref/release: 111 should result in downloading https://s3-us-west-2.amazonaws.com/human-pangenomics/pangenomes/freeze/freeze1/minigraph-cactus/hprc-v1.1-mc-grch38/hprc-v1.1-mc-grch38.gbz and the other index files for vg, see https://github.com/human-pangenomics/hpp_pangenome_resources.

Summary by CodeRabbit

• Chores
  • Updated the pangenome configuration to indicate release version "1.1" instead of using a direct data reference.
  • Improved configuration formatting for better consistency.

[coderabbitai]

Walkthrough

The pull request updates the pangenome configuration in the config/config.yaml file. Specifically, it removes the direct URL for pangenome haplotypes and introduces a new configuration parameter, release: "1.1", to version the pangenome resource. The TSV path for custom alignment properties remains unchanged and has been reformatted for consistency.

Changes

File(s)	Change Summary
config/config.yaml	- Removed the URL reference for pangenome haplotypes - Added release: "1.1" in the pangenome section - Reformatted the TSV path entry

Poem

I'm a rabbit with a joyful beat,
Hopping through configs, oh so neat!
No more URL, just version flair,
Carrots and code hop everywhere.
Leaping into updates with a happy heart,
CodeRabbit Inc. and I play our part!
🥕🐇

Tip

🌐 Web search-backed reviews and chat

• We have enabled web search-based reviews and chat for all users. This feature allows CodeRabbit to access the latest documentation and information on the web.
• You can disable this feature by setting web_search: false in the knowledge_base settings.
• Please share any feedback in the Discord discussion.

---

📜 Recent review details

Configuration used: CodeRabbit UI
Review profile: CHILL
Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between 84b6aed and d42116c.

📒 Files selected for processing (1)

• config/config.yaml (2 hunks)

🔇 Additional comments (2)

config/config.yaml (2)

32-32: New pangenome release version configuration added.
The addition of release: "1.1" in the pangenome section aligns well with the PR objective of downloading the pangenome indexes from HPRC. Ensure that downstream components or workflow steps correctly reference this parameter for fetching the proper index files.

---

291-291: Consistent formatting for custom alignment properties TSV path.
The reformatting of the TSV path to "config/alignment_properties.tsv" maintains consistency with the file structure. Since the value itself remains unchanged, no further action is required here.

---

Thank you for using CodeRabbit. We offer it for free to the OSS community and would appreciate your support in helping us grow. If you find it useful, would you consider giving us a shout-out on your favorite social media?

❤️ Share

• X
• Mastodon
• Reddit
• LinkedIn

🪧 Tips

Chat

There are 3 ways to chat with CodeRabbit:

• Review comments: Directly reply to a review comment made by CodeRabbit. Example:
  • I pushed a fix in commit <commit_id>, please review it.
  • Generate unit testing code for this file.
  • Open a follow-up GitHub issue for this discussion.
• Files and specific lines of code (under the "Files changed" tab): Tag @coderabbitai in a new review comment at the desired location with your query. Examples:
  • @coderabbitai generate unit testing code for this file.
  • @coderabbitai modularize this function.
• PR comments: Tag @coderabbitai in a new PR comment to ask questions about the PR branch. For the best results, please provide a very specific query, as very limited context is provided in this mode. Examples:
  • @coderabbitai gather interesting stats about this repository and render them as a table. Additionally, render a pie chart showing the language distribution in the codebase.
  • @coderabbitai read src/utils.ts and generate unit testing code.
  • @coderabbitai read the files in the src/scheduler package and generate a class diagram using mermaid and a README in the markdown format.
  • @coderabbitai help me debug CodeRabbit configuration file.

Note: Be mindful of the bot's finite context window. It's strongly recommended to break down tasks such as reading entire modules into smaller chunks. For a focused discussion, use review comments to chat about specific files and their changes, instead of using the PR comments.

CodeRabbit Commands (Invoked using PR comments)

• @coderabbitai pause to pause the reviews on a PR.
• @coderabbitai resume to resume the paused reviews.
• @coderabbitai review to trigger an incremental review. This is useful when automatic reviews are disabled for the repository.
• @coderabbitai full review to do a full review from scratch and review all the files again.
• @coderabbitai summary to regenerate the summary of the PR.
• @coderabbitai generate docstrings to generate docstrings for this PR. (Beta)
• @coderabbitai resolve resolve all the CodeRabbit review comments.
• @coderabbitai configuration to show the current CodeRabbit configuration for the repository.
• @coderabbitai help to get help.

Other keywords and placeholders

• Add @coderabbitai ignore anywhere in the PR description to prevent this PR from being reviewed.
• Add @coderabbitai summary to generate the high-level summary at a specific location in the PR description.
• Add @coderabbitai anywhere in the PR title to generate the title automatically.

CodeRabbit Configuration File (.coderabbit.yaml)

• You can programmatically configure CodeRabbit by adding a .coderabbit.yaml file to the root of your repository.
• Please see the configuration documentation for more information.
• If your editor has YAML language server enabled, you can add the path at the top of this file to enable auto-completion and validation: # yaml-language-server: $schema=https://coderabbit.ai/integrations/schema.v2.json

Documentation and Community

• Visit our Documentation for detailed information on how to use CodeRabbit.
• Join our Discord Community to get help, request features, and share feedback.
• Follow us on X/Twitter for updates and announcements.