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

Extending tests for sentieon joint germline AND avoiding duplicated variants in VQSR vcfs #1184

Merged
merged 19 commits into from
Aug 23, 2023
Merged

Extending tests for sentieon joint germline AND avoiding duplicated variants in VQSR vcfs #1184

merged 19 commits into from
Aug 23, 2023

Conversation

asp8200
Copy link
Contributor

@asp8200 asp8200 commented Aug 17, 2023 •
edited

Extending some CI-test for sentieon-based joint-germline. Inspired by what was done in PR #1173

Concerning VQSR in joint-germline subworkflows:

The following GATK-based joint-germline cmd results in the joint-germeline-vcf-file being sent through SNP and INDEL recalibration (VARIANTRECALIBRATOR and VQSR):

nextflow run main.nf -profile test_cache,tools_germline,docker --input ./tests/csv/3.0/mapped_joint_bam.csv --tools haplotypecaller --step variant_calling --joint_germline --outdir results2  -stub-run

Similarly for the Sentieon-based joint-germline cmd:

nextflow run main.nf -profile test_cache,tools_germline,docker --input ./tests/csv/3.0/mapped_joint_bam.csv --tools sentieon_haplotyper --step variant_calling --joint_germline --outdir results --sentieon_haplotyper_emit_mode gvcf -stub-run

It results in the joint-germeline-vcf-file being sent through SNP and INDEL recalibration (SENTIEON_VARCAL and SENTIEON_APPLYVARCAL):

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/sarek 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
Copy link

github-actions bot commented Aug 17, 2023 •
edited

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 3006118

+| ✅ 151 tests passed       |+
#| ❔   9 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.9
  • Run at 2023-08-22 14:48:36

@asp8200 asp8200 changed the title Extending tests for sentieon joint germline Extending tests for sentieon joint germline AND avoiding duplicated variants in VQSR vcfs Aug 17, 2023
@asp8200 asp8200 force-pushed the extending_tests_for_sentieon_joint_germline branch from 3914faa to a3f06f1 Compare August 22, 2023 12:57
@maxulysse
Copy link
Member

Looking good.
Can you update CHANGELOG?

maxulysse
maxulysse approved these changes Aug 22, 2023
View reviewed changes
Copy link
Member

@maxulysse maxulysse left a comment

Choose a reason for hiding this comment

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

LGTM

@asp8200 asp8200 marked this pull request as ready for review August 22, 2023 15:03
@maxulysse maxulysse merged commit a456c18 into dev Aug 23, 2023
25 checks passed
@asp8200 asp8200 deleted the extending_tests_for_sentieon_joint_germline branch August 23, 2023 10:21
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@maxulysse maxulysse maxulysse approved these changes

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

@adamrtalbot adamrtalbot Awaiting requested review from adamrtalbot

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
3 participants
@asp8200 @maxulysse @FriederikeHanssen