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

add bait regions to deepvariant for WES #633

Merged
merged 5 commits into from
Oct 16, 2024
Merged

add bait regions to deepvariant for WES #633

merged 5 commits into from
Oct 16, 2024

Conversation

ramprasadn
Copy link
Collaborator

PR checklist

Addresses #631

  • 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/raredisease 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>).
  • Ensure the test suite passes (nextflow run . -profile test_one_sample,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).

@ramprasadn ramprasadn mentioned this pull request Oct 14, 2024
Open
@github-actions GitHub Actions
Copy link

github-actions bot commented Oct 14, 2024 •
edited
Loading

nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 7e0cad7

+| ✅ 200 tests passed       |+
#| ❔   7 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

❔ Tests ignored:

  • files_exist - File is ignored: conf/modules.config
  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: assets/nf-core-raredisease_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-raredisease_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-raredisease_logo_dark.png
  • modules_config - modules_config

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2024-10-16 17:33:05

@ramprasadn ramprasadn marked this pull request as ready for review October 15, 2024 06:39
@fellen31
Copy link
Contributor

From the outside, something that's a bit unclear to me is the difference between call_intervals and --target_bed + --bait_padding.

jemten
jemten approved these changes Oct 16, 2024
View reviewed changes
Copy link
Collaborator

@jemten jemten left a comment

Choose a reason for hiding this comment

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

👍

@ramprasadn
Copy link
Collaborator Author

--call_intervals is only used by sentieon. I have clarified that in the schema now @fellen31

@ramprasadn ramprasadn merged commit cdf7263 into dev Oct 16, 2024
7 checks passed
@ramprasadn ramprasadn deleted the deepvar-for-regions branch October 17, 2024 06:49
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@jemten jemten jemten 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.
3 participants
@ramprasadn @fellen31 @jemten