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

58 test variant extractor for svs #60

Merged
merged 9 commits into from
Jul 9, 2024
Merged

58 test variant extractor for svs #60

merged 9 commits into from
Jul 9, 2024

Conversation

kubranarci
Copy link
Contributor

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/variantbenchmarking 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).

@kubranarci kubranarci linked an issue Jul 4, 2024 that may be closed by this pull request
test variant-extractor for SVs #58
Closed
@kubranarci kubranarci requested a review from nvnieuwk July 5, 2024 13:04
nvnieuwk
nvnieuwk reviewed Jul 5, 2024
View reviewed changes
Copy link
Contributor

@nvnieuwk nvnieuwk left a comment

Choose a reason for hiding this comment

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

Some comments although I didn't take a thorough look yet

assets/schema_input.json
Comment on lines -41 to -42
"minimum": 0,
"maximum": 1
Copy link
Contributor

Choose a reason for hiding this comment

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

You can keep these. they won't be validated if the value has not been given

Copy link
Contributor Author

Choose a reason for hiding this comment

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

I wanted to be safe 🗡️ ahaha

Copy link
Contributor

Choose a reason for hiding this comment

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

Don't worry it won't break anything :)

modules/local/variant_extractor/main.nf Show resolved Hide resolved
@kubranarci kubranarci requested a review from nvnieuwk July 8, 2024 09:10
nvnieuwk
nvnieuwk approved these changes Jul 9, 2024
View reviewed changes
Copy link
Contributor

@nvnieuwk nvnieuwk left a comment

Choose a reason for hiding this comment

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

It LGTM 🥳

@kubranarci kubranarci merged commit 9c90ba4 into dev Jul 9, 2024
4 checks passed
@kubranarci kubranarci deleted the 58-test-variant-extractor-for-svs branch July 9, 2024 08:21
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@nvnieuwk nvnieuwk nvnieuwk 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.

test variant-extractor for SVs
2 participants
@kubranarci @nvnieuwk