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

Added nf-tests to local subworkflows normalize and qc #94

Merged
merged 8 commits into from
Nov 19, 2024
Merged

Added nf-tests to local subworkflows normalize and qc #94

merged 8 commits into from
Nov 19, 2024

Conversation

nschcolnicov
Copy link

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/nanostring 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>).
  • 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).

@nschcolnicov nschcolnicov marked this pull request as ready for review November 14, 2024 18:01
This was referenced Nov 14, 2024
Closed
Closed
@nschcolnicov
Copy link
Author

linting not passing, we need to merge #82 first

atrigila
atrigila requested changes Nov 14, 2024
View reviewed changes
subworkflows/local/quality_control/tests/main.nf.test Outdated Show resolved Hide resolved
subworkflows/local/normalize/tests/main.nf.test.snap Outdated Show resolved Hide resolved
subworkflows/local/normalize/tests/main.nf.test Outdated Show resolved Hide resolved
@nschcolnicov nschcolnicov self-assigned this Nov 14, 2024
@nschcolnicov nschcolnicov mentioned this pull request Nov 14, 2024
Closed
@github-actions GitHub Actions
Copy link

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

nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 9862c18

+| ✅ 199 tests passed       |+
!| ❗   2 tests had warnings |!

❗ Test warnings:

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2024-11-19 12:06:31

atrigila
atrigila reviewed Nov 19, 2024
View reviewed changes
Copy link

@atrigila atrigila left a comment

Choose a reason for hiding this comment

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

great job, just a very minor comment

subworkflows/local/normalize/tests/main.nf.test Outdated
Comment on lines 28 to 30
workflow.out.normalized_counts,
workflow.out.normalized_counts_wo_HK,
workflow.out.versions
Copy link

Choose a reason for hiding this comment

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

Is there a reason why { assert snapshot(workflow.out).match() } is not used? You can check in one single command for all outputs.

subworkflows/local/quality_control/tests/main.nf.test
{ assert workflow.success},
{ assert snapshot(
workflow.out.nacho_qc_multiqc_metrics[0].collect { file(it).name }, //undeterministic .png mqc files
workflow.out.nacho_qc_multiqc_metrics[0].findAll { file(it).name.endsWith('.txt') }, //stable .txt mqc files
Copy link

Choose a reason for hiding this comment

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

Great job :)

@nschcolnicov
Copy link
Author

@atrigila All comments addressed, please re-review, thansk!

@nschcolnicov nschcolnicov merged commit 8efb6b1 into dev Nov 19, 2024
10 checks passed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@atrigila atrigila atrigila approved these changes

@alanmmobbs93 alanmmobbs93 Awaiting requested review from alanmmobbs93

Assignees

@nschcolnicov nschcolnicov

Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
2 participants
@nschcolnicov @atrigila