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

Update/gatk4spark applybqsr nftest #4613

Merged
merged 7 commits into from
Dec 19, 2023
Merged

Update/gatk4spark applybqsr nftest #4613

merged 7 commits into from
Dec 19, 2023

Conversation

anoronh4
Copy link
Contributor

@anoronh4 anoronh4 commented Dec 14, 2023 •
edited
Loading

PR checklist

Closes #4612
Also added a stub block!

  • 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 module conventions in the contribution docs
  • If necessary, include test data in your PR.
  • Remove all TODO statements.
  • Emit the versions.yml file.
  • Follow the naming conventions.
  • Follow the parameters requirements.
  • Follow the input/output options guidelines.
  • Add a resource label
  • Use BioConda and BioContainers if possible to fulfil software requirements.
  • Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
    • PROFILE=docker pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware
    • PROFILE=singularity pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware
    • PROFILE=conda pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware

@anoronh4
Copy link
Contributor Author

i think i may have accidentally checked out a branch that started from gatk4/baserecalibrator. if the PR #4611 is approved first then it might not be necessary to rework this PR?? let me know.

@anoronh4 anoronh4 marked this pull request as draft December 15, 2023 02:28
SPPearce
SPPearce approved these changes Dec 19, 2023
View reviewed changes
Copy link
Contributor

@SPPearce SPPearce left a comment •
edited
Loading

Choose a reason for hiding this comment

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

Looks good to me, I think we can just merge the two modules changes together and close the other. They are related tools and you're only updating the tests so I don't mind several modules together like this.

@SPPearce SPPearce mentioned this pull request Dec 19, 2023
Closed
14 tasks
@anoronh4 anoronh4 marked this pull request as ready for review December 19, 2023 15:53
@anoronh4 anoronh4 enabled auto-merge December 19, 2023 15:54
@anoronh4 anoronh4 added this pull request to the merge queue Dec 19, 2023
Merged via the queue into master with commit 85561f4 Dec 19, 2023
15 checks passed
@anoronh4 anoronh4 linked an issue Dec 19, 2023 that may be closed by this pull request
[FEATURE] gatk4/baserecalibrator nf-test #4608
Closed
lrauschning pushed a commit to lrauschning/modules that referenced this pull request Dec 21, 2023
@anoronh4 @lrauschning
Update/gatk4spark applybqsr nftest (nf-core#4613)
cb00d92 
* remove pytests

* removed TODO statements

* add stub block

* add nf-tests

* remove pytests
lrauschning pushed a commit to lrauschning/modules that referenced this pull request Jan 17, 2024
@anoronh4 @lrauschning
Update/gatk4spark applybqsr nftest (nf-core#4613)
9f8cc1a 
* remove pytests

* removed TODO statements

* add stub block

* add nf-tests

* remove pytests
@maxulysse maxulysse deleted the update/gatk4spark_applybqsr_nftest branch January 18, 2024 11:03
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@SPPearce SPPearce SPPearce approved these changes

@yocra3 yocra3 Awaiting requested review from yocra3

@FriederikeHanssen FriederikeHanssen Awaiting requested review from FriederikeHanssen

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

Assignees
No one assigned
Labels
nf-test ready to merge
Projects
nf-test Migration
Status: Done
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.

[FEATURE] add nf-tests to gatk4spark/applybqsr [FEATURE] gatk4/baserecalibrator nf-test
2 participants
@anoronh4 @SPPearce