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

Fix stack overflow #371

Merged
merged 2 commits into from
Nov 22, 2023
Merged

Fix stack overflow #371

merged 2 commits into from
Nov 22, 2023

Conversation

krokicki
Copy link

This PR addresses #370. In summary, PHANTOMPEAKQUALTOOLS throws a stack overflow exception on certain types of input data. This issue suggests a fix by increasing the default --max-ppsize. This is already implemented in MULTIQC_CUSTOM_PHANTOMPEAKQUALTOOLS. I just added the same parameter to PHANTOMPEAKQUALTOOLS via the modules.conf. This allows the pipeline to run successfully on our data.

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/chipseq 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 GitHub Actions
Copy link

github-actions bot commented Nov 22, 2023 •
edited

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 0bb54eb

+| ✅ 159 tests passed       |+
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • 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 WorkflowChipseq.groovy: Optionally add in-text citation tools to this list.

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-11-22 18:45:12

JoseEspinosa
JoseEspinosa approved these changes Nov 22, 2023
View reviewed changes
Copy link
Member

@JoseEspinosa JoseEspinosa left a comment

Choose a reason for hiding this comment

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

Awesome! 😄
LGTM 🚀

@JoseEspinosa JoseEspinosa merged commit 9eee551 into nf-core:dev Nov 22, 2023
11 checks passed
@krokicki krokicki mentioned this pull request Nov 27, 2023
Closed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@JoseEspinosa JoseEspinosa JoseEspinosa 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.

None yet
2 participants
@krokicki @JoseEspinosa