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Updates suggested by @muffato #49

Merged
merged 2 commits into from
Dec 13, 2024
Merged

Updates suggested by @muffato #49

merged 2 commits into from
Dec 13, 2024

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DLBPointon
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Changes suggested by @muffato, I don't expect this to change any of the tests passing.

@DLBPointon DLBPointon requested a review from muffato December 12, 2024 11:45
@DLBPointon DLBPointon self-assigned this Dec 12, 2024
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github-actions bot commented Dec 12, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 88aea92

+| ✅ 122 tests passed       |+
#| ❔  22 tests were ignored |#
!| ❗  10 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: .github/workflows/awstest.yml
  • files_exist - File not found: .github/workflows/awsfulltest.yml
  • nextflow_config - Config manifest.version should end in dev: '1.1.0'
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in README.md: Include a figure that guides the user through the major workflow steps. Many nf-core
  • pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
  • 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
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • schema_lint - Input mimetype is missing or empty

❔ Tests ignored:

  • files_exist - File is ignored: assets/multiqc_config.yml
  • files_exist - File is ignored: assets/nf-core-curationpretext_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-curationpretext_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-curationpretext_logo_dark.png
  • 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/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: .github/workflows/branch.yml
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • files_unchanged - File ignored due to lint config: assets/email_template.txt
  • files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
  • files_unchanged - File does not exist: assets/nf-core-curationpretext_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-curationpretext_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-curationpretext_logo_dark.png
  • files_unchanged - File ignored due to lint config: docs/README.md
  • 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/curationpretext/curationpretext/.github/workflows/awstest.yml
  • multiqc_config - 'assets/multiqc_config.yml' not found

✅ Tests passed:

Run details

  • nf-core/tools version 2.8
  • Run at 2024-12-12 11:47:15

@DLBPointon DLBPointon mentioned this pull request Dec 12, 2024
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@muffato muffato merged commit faa038e into dev Dec 13, 2024
6 checks passed
@muffato muffato deleted the dev_main_update branch December 13, 2024 12:31
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@muffato muffato muffato approved these changes

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@DLBPointon @muffato