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Update SRA workflow tests #191

Merged
merged 22 commits into from
Aug 29, 2023
Merged

Update SRA workflow tests #191

merged 22 commits into from
Aug 29, 2023

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maxulysse
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github-actions bot commented Aug 25, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 57bf167

+| ✅ 134 tests passed       |+
#| ❔  13 tests were ignored |#
!| ❗   7 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • files_exist - File not found: .github/workflows/awstest.yml
  • files_exist - File not found: .github/workflows/awsfulltest.yml
  • files_exist - File not found: lib/WorkflowFetchngs.groovy
  • nextflow_config - Config manifest.version should end in dev: 1.10.1
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline
  • schema_description - No description provided in schema for parameter: dbgap_key

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.9
  • Run at 2023-08-28 13:44:50

@maxulysse
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remember to remove profile test when doing tests in the GHA

@maxulysse
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Problem with sorting of channel within nf-test, so testing instead the files for now.

@maxulysse
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Move forward into modularization of the workflows.
Idea would be to push them to local subworkflows.
Move the libs either in the newly created subworkflow or in the main workflow.groovy

@maxulysse maxulysse changed the title WIP: test workflows Update SRA workflow tests Aug 28, 2023
@maxulysse maxulysse mentioned this pull request Aug 28, 2023
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@maxulysse
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self-merging, will fix the failing tests separately

@maxulysse maxulysse merged commit 3b6ec04 into nf-core:refactor Aug 29, 2023
@maxulysse maxulysse deleted the better_tests branch August 29, 2023 08:30
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@adamrtalbot adamrtalbot adamrtalbot approved these changes

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@maxulysse @adamrtalbot