fix openms singularity url in dev.conf

[jpfeuffer]

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/quantms branch on the nf-core/test-datasets repository.
• Make sure your code lints (nf-core lint).
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

Summary by CodeRabbit

• New Features

  • Enhanced support for multiple container engines (Singularity and Apptainer) in the configuration.
  • Updated container image paths for improved flexibility and access to new registry images.

• Bug Fixes

  • Resolved issues related to container selection logic to ensure proper image retrieval based on the container engine used.

[coderabbitai]

Walkthrough

The changes in this pull request involve modifications to the conf/dev.config file for a Nextflow process named openms. The primary adjustment is in the logic for selecting the appropriate container image based on the container engine used. The updated configuration now recognizes both 'singularity' and 'apptainer' as valid container engines and updates the paths to the container images accordingly, allowing for greater flexibility in container management.

Changes

File	Change Summary
conf/dev.config	Modified the container logic to include 'apptainer' as a valid engine; updated image paths to new registry and names.

Sequence Diagram(s)

sequenceDiagram
    participant User
    participant Nextflow
    participant ContainerRegistry

    User->>Nextflow: Start workflow
    Nextflow->>ContainerRegistry: Check container engine
    alt Singularity or Apptainer
        Nextflow->>ContainerRegistry: Select image oras://ghcr.io/openms/openms-tools-thirdparty-sif:latest
    else Fallback
        Nextflow->>ContainerRegistry: Select image ghcr.io/openms/openms-tools-thirdparty:latest
    end
    Nextflow->>User: Workflow running with selected container

Loading

🐰 "In the garden where containers play,
Apptainer joins the fray today.
With images bright from a new domain,
Flexibility blooms, no need for disdain.
Singularity smiles, together they thrive,
In a world of workflows, they come alive!" 🌼

---

📜 Recent review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Reviewing files that changed from the base of the PR and between b7c9b6a and 801181a.

📒 Files selected for processing (1)

• conf/dev.config (1 hunks)

🔇 Additional comments (1)

conf/dev.config (1)

22-22: LGTM! The container configuration has been improved.

The changes make two important improvements:

1. Added support for the Apptainer container engine alongside Singularity
2. Updated to use the ORAS protocol for container distribution, which is the recommended approach for OCI artifacts

Let's verify the container image accessibility:

---

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 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.