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Merged
danilodileo merged 12 commits into from
May 23, 2024
Merged

Update doc #56

danilodileo merged 12 commits into from
May 23, 2024

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@danilodileo
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@danilodileo danilodileo commented May 16, 2024

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).

I updated the documentation for both output.md and usage.md

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github-actions bot commented May 16, 2024 •
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nf-core lint overall result: Failed ❌

Posted for pipeline commit 7bface2

+| ✅ 187 tests passed       |+
!| ❗  30 tests had warnings |!
-| ❌   5 tests failed       |-
Details

❌ Test failures:

  • files_unchanged - .github/PULL_REQUEST_TEMPLATE.md does not match the template
  • files_unchanged - .github/workflows/linting_comment.yml does not match the template
  • files_unchanged - .github/workflows/linting.yml 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:

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-05-23 08:53:38

erikrikarddaniel
erikrikarddaniel approved these changes May 22, 2024
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There are a few remaining things -- among them to properly explain how the selection of genomes work -- but I realize I need to sit down with the whole files. I therefore approved now -- with some comments -- and will open a PR later with my modifications.

@danilodileo danilodileo merged commit ad01339 into nf-core:dev May 23, 2024
@danilodileo danilodileo deleted the update-doc branch May 24, 2024 07:54
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