Skip to content
New issue

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

#

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

Already on GitHub? # 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
Contributor

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
Loading

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
# for free to join this conversation on GitHub. Already have an account? # 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.
2 participants
@krokicki @JoseEspinosa