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

Allow dbsnp if null in germline variant calling #1628

Merged
merged 3 commits into from
Aug 23, 2024
Merged

Allow dbsnp if null in germline variant calling #1628

merged 3 commits into from
Aug 23, 2024

Conversation

cmatKhan
Copy link
Contributor

closes #1550

This adjusts the channel mapping of dbsnp and dbsnp_tbi in the germline variant calling subworkflow to match the same call int he sentieon subworkflow.

This fixes a bug when doing at least single sample variant calling (rather than joint) on a run/organism that does not have a dbsnp file provided.

@cmatKhan
this adjusts the dbsnp channel mapping in variant_calling_germline_al…
c9a55b8 
…l to match variant_calling_sentieon_dnascope. null values are handled appropriately this way
@github-actions GitHub Actions
Copy link

github-actions bot commented Aug 21, 2024 •
edited
Loading

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit e0cbf05

+| ✅ 200 tests passed       |+
#| ❔  12 tests were ignored |#
!| ❗   3 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!

❔ Tests ignored:

  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • files_exist - File is ignored: .github/workflows/awstest.yml
  • files_exist - File is ignored: conf/modules.config
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: assets/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_dark.png
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore
  • actions_ci - actions_ci
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/sarek/sarek/.github/workflows/awstest.yml
  • template_strings - template_strings
  • modules_config - modules_config

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-08-22 18:09:44

@cmatKhan cmatKhan linked an issue Aug 21, 2024 that may be closed by this pull request
single sample haplotypecaller with no dbsnp causes error because of missing dbsnp_tbi #1550
Closed
FriederikeHanssen
FriederikeHanssen previously approved these changes Aug 22, 2024
View reviewed changes
Copy link
Contributor

@FriederikeHanssen FriederikeHanssen left a comment

Choose a reason for hiding this comment

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

Nice, thank you 🚀

FriederikeHanssen
FriederikeHanssen reviewed Aug 22, 2024
View reviewed changes
CHANGELOG.md Outdated Show resolved Hide resolved
@cmatKhan @FriederikeHanssen
fix type on 1628 entry in changelog
e0cbf05 
Co-authored-by: Friederike Hanssen <friederike.hanssen@seqera.io>
FriederikeHanssen
FriederikeHanssen approved these changes Aug 23, 2024
View reviewed changes
Copy link
Contributor

@FriederikeHanssen FriederikeHanssen left a comment

Choose a reason for hiding this comment

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

Feel free to merge!

@cmatKhan cmatKhan merged commit 7871b03 into nf-core:dev Aug 23, 2024
45 checks passed
@cmatKhan cmatKhan deleted the fix_dbsnp_if_null branch August 23, 2024 18:53
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@FriederikeHanssen FriederikeHanssen FriederikeHanssen approved these changes

@maxulysse maxulysse Awaiting requested review from maxulysse maxulysse is a code owner

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

Successfully merging this pull request may close these issues.

single sample haplotypecaller with no dbsnp causes error because of missing dbsnp_tbi
2 participants
@cmatKhan @FriederikeHanssen