Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Revert thermorawfileparser #433

Merged
merged 3 commits into from
Oct 23, 2024
Merged

Revert thermorawfileparser #433

merged 3 commits into from
Oct 23, 2024

Conversation

daichengxin
Copy link
Collaborator

@daichengxin daichengxin commented Oct 23, 2024 •
edited by codiumai-pr-agent-pro bot
Loading

User description

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).

PR Type

enhancement

Description

  • Reverted the thermorawfileparser version from 1.4.5 to 1.3.4 in the Nextflow process configuration.
  • Updated the container image references to align with the reverted version, ensuring compatibility and stability.

Changes walkthrough 📝

Relevant files
Enhancement
main.nf
Revert thermorawfileparser to version 1.3.4                           

modules/local/thermorawfileparser/main.nf

  • Reverted thermorawfileparser version from 1.4.5 to 1.3.4.
  • Updated container image references to match the reverted version.
    		•  +3/-3     

    💡 PR-Agent usage: Comment /help "your question" on any pull request to receive relevant information

    @codiumai-pr-agent-pro CodiumAI PR-Agent Pro
    Copy link

    PR-Agent was enabled for this repository. To continue using it, please link your git user with your CodiumAI identity here.

    PR Reviewer Guide 🔍

    Here are some key observations to aid the review process:

    ⏱️ Estimated effort to review: 2 🔵🔵⚪⚪⚪
    🧪 No relevant tests
    🔒 No security concerns identified
    ⚡ Recommended focus areas for review

    Version Compatibility
    Ensure that reverting to ThermoRawFileParser version 1.3.4 does not introduce compatibility issues with other components of the pipeline or break any existing functionality.

    @codiumai-pr-agent-pro CodiumAI PR-Agent Pro
    Copy link

    PR-Agent was enabled for this repository. To continue using it, please link your git user with your CodiumAI identity here.

    PR Code Suggestions ✨

    No code suggestions found for the PR.

    @github-actions GitHub Actions
    Copy link

    github-actions bot commented Oct 23, 2024 •
    edited
    Loading

    nf-core pipelines lint overall result: Passed ✅ ⚠️

    Posted for pipeline commit 827f3e6

    +| ✅ 107 tests passed       |+
#| ❔  13 tests were ignored |#
!| ❗  11 tests had warnings |!

    ❗ Test warnings:

    • pipeline_todos - TODO string in nextflow.config: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
    • pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
    • pipeline_todos - TODO string in README.md: Add bibliography of tools and data used in your pipeline
    • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
    • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
    • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
    • pipeline_todos - TODO string in base.config: Check the defaults for all processes
    • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
    • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
    • pipeline_todos - TODO string in ci.yml: You can customise CI pipeline run tests as required
    • pipeline_todos - TODO string in ci.yml: You can customise CI pipeline run tests as required

    ❔ Tests ignored:

    ✅ Tests passed:

    Run details

    • nf-core/tools version 3.0.2
    • Run at 2024-10-23 07:47:40

    @daichengxin
    Copy link
    Collaborator Author

    This PR is related #432, even #431

    @jpfeuffer
    Copy link
    Collaborator

    jpfeuffer commented Oct 23, 2024 via email •
    edited
    Loading

    @ypriverol ypriverol self-requested a review October 23, 2024 09:09
    @ypriverol ypriverol merged commit c70bc99 into bigbio:dev Oct 23, 2024
    21 checks passed
    Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
    Reviewers

    @jpfeuffer jpfeuffer jpfeuffer approved these changes

    @ypriverol ypriverol ypriverol approved these changes

    Assignees
    No one assigned
    Labels
    enhancement New feature or request Review effort [1-5]: 2
    Projects
    None yet
    Milestone
    No milestone
    Development

    Successfully merging this pull request may close these issues.
    3 participants
    @daichengxin @jpfeuffer @ypriverol