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

Fixing call to GATK4_HAPLOTYPECALLER #1488

Merged
merged 2 commits into from
Apr 29, 2024
Merged

Fixing call to GATK4_HAPLOTYPECALLER #1488

merged 2 commits into from
Apr 29, 2024

Conversation

asp8200
Copy link
Contributor

@asp8200 asp8200 commented Apr 29, 2024 •
edited
Loading

The test-profile test_full_germline isn't working on Sarek v3.4.1. The problem seems to be that the input-channel dbsnp_tbi is a queue channel and not a value channel, so the process GATK4_HAPLOTYPECALLER is only executed once instead of for each interval.

I added .collect() to the definition of channels. That should force the channels to be interpreted as value channels.

The following test passed:

nextflow run main.nf -profile test_full_germline,docker --outdir out --tools haplotypecaller

Had some "resource-issues" with running the full germline test, ie.

nextflow run main.nf -profile test_full_germline,docker --outdir out

so that test is still running. ...

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 (nf-test test tests/ --verbose --profile +docker).
  • 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).

@github-actions GitHub Actions
Copy link

github-actions bot commented Apr 29, 2024 •
edited
Loading

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit eaa1373

+| ✅ 181 tests passed       |+
#| ❔  14 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_exist - File is ignored: lib/WorkflowMain.groovy
  • files_exist - File is ignored: lib/NfcoreTemplate.groovy
  • files_exist - File is ignored: lib/WorkflowSarek.groovy
  • 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 or pyproject.toml
  • actions_ci - actions_ci
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/sarek/sarek/.github/workflows/awstest.yml
  • template_strings - template_strings

✅ Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-04-29 06:06:08

@asp8200 asp8200 marked this pull request as ready for review April 29, 2024 06:15
@maxulysse maxulysse merged commit 3fd2743 into nf-core:dev Apr 29, 2024
21 checks passed
@asp8200 asp8200 deleted the fixing_test_full_germline branch April 29, 2024 07:36
@asp8200
Copy link
Contributor Author

asp8200 commented Apr 29, 2024

Okay to merge. The full germline test is almost done, just missing one of the expected six executions of VEP:

image

@asp8200
Copy link
Contributor Author

asp8200 commented Apr 29, 2024

Full germline test done:

image

@asp8200 asp8200 mentioned this pull request May 2, 2024
Closed
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

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
@asp8200 @maxulysse