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

Fixed extra flag setting for ms2pip #275

Merged
merged 3 commits into from
Aug 18, 2023
Merged

Fixed extra flag setting for ms2pip #275

merged 3 commits into from
Aug 18, 2023

Conversation

steffenlem
Copy link
Contributor

The -extra flag in the PSMFeatureExtractor is now set if either ms2pip or deeplc are selected.

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/mhcquant 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>).
  • 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).

@github-actions
Copy link

github-actions bot commented Jul 11, 2023 •
edited
Loading

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 047c8d8

+| ✅ 156 tests passed       |+
!| ❗   7 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in README.md: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
  • pipeline_todos - TODO string in README.md: update the following command to include all required parameters for a minimal example
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • system_exit - System.exit in WorkflowMain.groovy: System.exit(1) [line 51]
  • system_exit - System.exit in WorkflowMhcquant.groovy: System.exit(1) [line 18]
  • system_exit - System.exit in WorkflowMhcquant.groovy: System.exit(1) [line 45]
  • system_exit - System.exit in WorkflowMhcquant.groovy: System.exit(1) [line 51]

✅ Tests passed:

Run details

  • nf-core/tools version 2.9
  • Run at 2023-08-18 10:05:56

jonasscheid
jonasscheid requested changes Aug 15, 2023
View reviewed changes
Copy link
Collaborator

@jonasscheid jonasscheid left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Change params as requested then 👍🏼

modules/local/openms_psmfeatureextractor.nf Outdated Show resolved Hide resolved
@jonasscheid jonasscheid merged commit 013dc25 into nf-core:dev Aug 18, 2023
8 checks passed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@jonasscheid jonasscheid jonasscheid approved these changes

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
2 participants
@steffenlem @jonasscheid