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Template 3.0.2 update #94

Merged
merged 18 commits into from
Jan 17, 2025
Merged

Template 3.0.2 update #94

merged 18 commits into from
Jan 17, 2025

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danilodileo
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@danilodileo danilodileo commented Dec 11, 2024 •
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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).
  • 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).

There are quite a lot of files but most is modules update

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This PR is against the master branch ❌

  • Do not close this PR
  • Click Edit and change the base to dev
  • This CI test will remain failed until you push a new commit

Hi @danilodileo,

It looks like this pull-request is has been made against the danilodileo/magmap master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the danilodileo/magmap dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

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github-actions bot commented Dec 11, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 93dd8c1

+| ✅ 213 tests passed       |+
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • 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 citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2025-01-17 11:21:08

@erikrikarddaniel erikrikarddaniel changed the base branch from master to dev December 11, 2024 18:17
@danilodileo
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@erikrikarddaniel There is only one thing failing but my guess is the template from the new template update

@erikrikarddaniel
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There are some new linting errors (incorrect template files) and some warnings. We should make sure to get rid of the warnings. The genomes, igenomes things should be just by adding them to some file (forgot which) that contain skipped parameters.

@danilodileo
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There are some new linting errors (incorrect template files) and some warnings. We should make sure to get rid of the warnings. The genomes, igenomes things should be just by adding them to some file (forgot which) that contain skipped parameters.

Not it is fixed :)

erikrikarddaniel
erikrikarddaniel approved these changes Dec 16, 2024
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There are a couple of igenomes files, maybe we could get rid of them?

@danilodileo @erikrikarddaniel
Update docs/usage.md
93dd8c1 
Co-authored-by: Daniel Lundin <erik.rikard.daniel@gmail.com>
@danilodileo danilodileo merged commit 1a82e21 into nf-core:dev Jan 17, 2025
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@danilodileo danilodileo deleted the template-3.0.2-update branch January 17, 2025 11:20
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@erikrikarddaniel erikrikarddaniel erikrikarddaniel approved these changes

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@danilodileo @erikrikarddaniel