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Improve GHA CI workflow step name #15

Merged
merged 1 commit into from
Apr 30, 2024
Merged

Improve GHA CI workflow step name #15

merged 1 commit into from
Apr 30, 2024

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scwatts
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@scwatts scwatts commented Apr 26, 2024

  • the GHA CI job runs only stubs rather than with actual test data due to disk limitations of GHA runner instances
  • job step name: Run pipeline with test data → Run pipeline stubs

@scwatts scwatts requested a review from charlesshale April 26, 2024 01:15
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github-actions bot commented Apr 26, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit d47abdc

+| ✅ 155 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗  45 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: assets/multiqc_config.yml
  • nextflow_config - Config manifest.version should end in dev: 0.3.1
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
  • pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed
  • pipeline_todos - TODO string in output.md: Write this documentation describing your workflow's output
  • pipeline_todos - TODO string in usage.md: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website.
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • 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!
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • system_exit - System.exit in main.nf: System.exit(1) [line 44]
  • system_exit - System.exit in main.nf: System.exit(1) [line 46]
  • system_exit - System.exit in Processes.groovy: System.exit(1) [line 33]
  • system_exit - System.exit in Processes.groovy: System.exit(1) [line 49]
  • system_exit - System.exit in WorkflowOncoanalyser.groovy: System.exit(1) [line 62]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 29]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 39]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 47]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 55]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 63]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 68]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 84]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 89]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 108]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 113]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 121]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 182]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 263]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 275]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 283]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 290]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 298]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 313]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 344]
  • system_exit - System.exit in WorkflowMain.groovy: System.exit(1) [line 116]
  • system_exit - System.exit in WorkflowMain.groovy: System.exit(1) [line 123]
  • system_exit - System.exit in WorkflowMain.groovy: System.exit(1) [line 130]
  • system_exit - System.exit in WorkflowMain.groovy: System.exit(1) [line 144]
  • system_exit - System.exit in WorkflowMain.groovy: System.exit(1) [line 154]
  • system_exit - System.exit in WorkflowMain.groovy: System.exit(1) [line 159]
  • system_exit - System.exit in WorkflowMain.groovy: System.exit(1) [line 172]
  • system_exit - System.exit in WorkflowMain.groovy: System.exit(1) [line 188]
  • system_exit - System.exit in WorkflowMain.groovy: System.exit(1) [line 197]

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-04-26 01:17:47

@scwatts scwatts merged commit 44cc52e into dev Apr 30, 2024
4 checks passed
@scwatts scwatts deleted the rename-ci-job-step branch April 30, 2024 01:24
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@charlesshale charlesshale charlesshale approved these changes

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@scwatts @charlesshale