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Update modules #37

Merged
merged 12 commits into from
Feb 20, 2024
Merged

Update modules #37

merged 12 commits into from
Feb 20, 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 (nextflow run . -profile 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).

I updated the modules and the template. I took a look at this issue #36 and the trimming option is working

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github-actions bot commented Feb 20, 2024 •
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nf-core lint overall result: Failed ❌

Posted for pipeline commit b6ce048

+| ✅ 166 tests passed       |+
!| ❗  13 tests had warnings |!
-| ❌   3 tests failed       |-

❌ Test failures:

  • files_unchanged - assets/nf-core-magmap_logo_light.png does not match the template
  • 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 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 WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
  • 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
  • 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
  • schema_description - No description provided in schema for parameter: sourmash

✅ Tests passed:

Run details

  • nf-core/tools version 2.12.1
  • Run at 2024-02-20 12:33:04

erikrikarddaniel
erikrikarddaniel approved these changes Feb 20, 2024
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👍

@danilodileo danilodileo merged commit 7e72cd5 into nf-core:dev Feb 20, 2024
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@danilodileo danilodileo mentioned this pull request Feb 20, 2024
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@danilodileo danilodileo deleted the update_modules branch February 21, 2024 12:56
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@erikrikarddaniel erikrikarddaniel erikrikarddaniel approved these changes

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@danilodileo @erikrikarddaniel