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Will's Update to MerquryFK #344

Merged
merged 9 commits into from
Dec 10, 2024
Merged

Will's Update to MerquryFK #344

merged 9 commits into from
Dec 10, 2024

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DLBPointon
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github-actions bot commented Dec 9, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit c55ea9b

+| ✅ 127 tests passed       |+
#| ❔  20 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: '1.2.0'
  • 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
  • pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
  • system_exit - System.exit in WorkflowTreeval.groovy: System.exit(1) [line 17]

❔ Tests ignored:

  • files_exist - File is ignored: assets/nf-core-treeval_logo_light.png
  • files_exist - File is ignored: conf/test_full.config
  • files_exist - File is ignored: docs/images/nf-core-treeval_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-treeval_logo_dark.png
  • files_exist - File is ignored: conf/igenomes.config
  • files_exist - File is ignored: .github/workflows/awstest.yml
  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • nextflow_config - Config variable ignored: manifest.name
  • nextflow_config - Config variable ignored: manifest.homePage
  • files_unchanged - File ignored due to lint config: LICENSE or LICENSE.md or LICENCE or LICENCE.md
  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
  • files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
  • files_unchanged - File does not exist: assets/nf-core-treeval_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-treeval_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-treeval_logo_dark.png
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/treeval/treeval/.github/workflows/awstest.yml

✅ Tests passed:

Run details

  • nf-core/tools version 2.8
  • Run at 2024-12-09 16:30:25

@DLBPointon DLBPointon mentioned this pull request Dec 9, 2024
Closed
9 tasks
This was linked to issues Dec 10, 2024
Treeval pipeline usage has a mistake #342
Open
ERROR ~ No such variable: coverage_report #343
Open
@weaglesBio weaglesBio merged commit 007cb12 into dev Dec 10, 2024
6 checks passed
@weaglesBio weaglesBio deleted the tola406_genesetsyntenyyaml branch December 10, 2024 09:57
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@weaglesBio weaglesBio weaglesBio approved these changes

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ERROR ~ No such variable: coverage_report Treeval pipeline usage has a mistake
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@DLBPointon @weaglesBio