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Update docs #283

Merged
merged 6 commits into from
Apr 10, 2024
Merged

Update docs #283

merged 6 commits into from
Apr 10, 2024

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danilodileo
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@danilodileo danilodileo commented Apr 10, 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/metatdenovo 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>).
  • 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).

I updated the documentation based on issues #281 and #273

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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/metatdenovo 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/metatdenovo 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 Apr 10, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 4f7826a

+| ✅ 180 tests passed       |+
!| ❗   3 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.
  • system_exit - System.exit in NfcoreSchema.groovy: System.exit(1) [line 180]

✅ Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-04-10 13:06:43

@danilodileo danilodileo changed the base branch from master to dev April 10, 2024 12:33
@erikrikarddaniel
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This is against master, that's not your intention, right?

erikrikarddaniel
erikrikarddaniel approved these changes Apr 10, 2024
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@erikrikarddaniel erikrikarddaniel left a comment

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Two small suggestions, otherwise 👍

README.md Outdated Show resolved Hide resolved
docs/usage.md Outdated Show resolved Hide resolved
@danilodileo
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This is against master, that's not your intention, right?

I changed it!

danilodileo and others added 3 commits April 10, 2024 14:55
@danilodileo @erikrikarddaniel
Update README.md
ed740f8 
Co-authored-by: Daniel Lundin <[email protected]>
@danilodileo @erikrikarddaniel
Update docs/usage.md
5dd427a 
Co-authored-by: Daniel Lundin <[email protected]>
updated docs
4f7826a
@danilodileo danilodileo merged commit b3f2324 into nf-core:dev Apr 10, 2024
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This was referenced Apr 10, 2024
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@danilodileo danilodileo deleted the update-docs branch April 25, 2024 11:40
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@erikrikarddaniel erikrikarddaniel erikrikarddaniel approved these changes

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@danilodileo @erikrikarddaniel