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Template update 2.14.1 #57

Merged
merged 12 commits into from
Jun 12, 2024
Merged

Template update 2.14.1 #57

merged 12 commits into from
Jun 12, 2024

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danilodileo
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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/magmap branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nf-test test main.nf.test -profile test,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).

Template update 2.14.1

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github-actions bot commented May 24, 2024 •
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nf-core lint overall result: Failed ❌

Posted for pipeline commit 0d0a1ed

+| ✅ 190 tests passed       |+
!| ❗   9 tests had warnings |!
-| ❌   2 tests failed       |-

❌ Test failures:

  • files_unchanged - docs/images/nf-core-magmap_logo_light.png does not match the template
  • files_unchanged - docs/images/nf-core-magmap_logo_dark.png does not match the template

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • 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: Add full-sized test dataset and amend the paragraph below if applicable
  • pipeline_todos - TODO string in README.md: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
  • 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 README.md: Add bibliography of tools and data used in your pipeline
  • 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
  • pipeline_todos - TODO string in ci.yml: You can customise CI pipeline run tests as required
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-06-12 15:27:00

erikrikarddaniel
erikrikarddaniel approved these changes May 24, 2024
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👍

erikrikarddaniel
erikrikarddaniel approved these changes Jun 12, 2024
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One small question.

.github/PULL_REQUEST_TEMPLATE.md
@@ -18,7 +18,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/magm
- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/magmap/tree/master/.github/CONTRIBUTING.md)
- [ ] If necessary, also make a PR on the nf-core/magmap _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
- [ ] Make sure your code lints (`nf-core lint`).
- [ ] Ensure the test suite passes (`nf-test test main.nf.test -profile test,docker`).
- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
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Is this because we haven't implemented nf-test yet?

@danilodileo danilodileo merged commit c466fc2 into nf-core:dev Jun 12, 2024
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@danilodileo danilodileo mentioned this pull request Jun 12, 2024
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@danilodileo danilodileo deleted the template-update-2.14.1 branch June 13, 2024 09:56
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@danilodileo @erikrikarddaniel