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add test data in igenomes #1489

Merged
merged 14 commits into from
Apr 30, 2024
Merged

add test data in igenomes #1489

merged 14 commits into from
Apr 30, 2024

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maxulysse
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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).

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github-actions bot commented Apr 29, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit c7b428b

+| ✅ 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 20:10:48

@asp8200
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asp8200 commented Apr 29, 2024

I know this is just a draft, but I see failing tests

@maxulysse
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I know this is just a draft, but I see failing tests

Patience young padawan

@maxulysse maxulysse marked this pull request as ready for review April 29, 2024 14:41
@asp8200
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asp8200 commented Apr 30, 2024

So it seems that in the test-profile you now fetch test-data from s3://ngi-igenomes/testdata/nf-core/modules instead of from https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/ - what is the advantage with that approach? And why isn't the same approach used for, say, test_full and test_full_germline?

@maxulysse
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That resolves to the same actually.
We can actually use any path

@asp8200
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asp8200 commented Apr 30, 2024 •
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I still don't understand what the purpose of this PR is. What does it fix? What does it improve?

@maxulysse
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So before we were only using params directly to assign reference files.
Now with this one we mix in depending on the tests using igenomes with the newly created key, and params with or without igenomes.
This should allow us to detect cardinality errors and queue/value channel errors depending on the origin of the reference files.

@maxulysse maxulysse merged commit e0517a5 into nf-core:dev Apr 30, 2024
83 checks passed
@maxulysse maxulysse deleted the igemomes_tests branch April 30, 2024 08:38
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@asp8200 asp8200 asp8200 approved these changes

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

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@maxulysse @asp8200