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Adding Variant Calling tutorial pages to Usage section #1706

Merged
merged 7 commits into from
Oct 29, 2024
Merged

Adding Variant Calling tutorial pages to Usage section #1706

merged 7 commits into from
Oct 29, 2024

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lescai
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@lescai lescai commented Oct 28, 2024 •
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PR checklist

  • this is a documentation PR
  • it is meant to add a specific tutorial about variant calling with sarek
  • it is based on a published and tested tutorial to run entirely on gitpod

WARNING:
nf-core website code "pipelines.json" file must be changed to account for the file path as

"doc_files": [
                        "docs/output.md",
                        "docs/usage.md",
                        "docs/usage/variantcalling/introduction.md",
                        "docs/usage/variantcalling/theory.md",
                        "docs/usage/variantcalling/sarek.md",
                        "docs/usage/variantcalling/interpretation.md"
                    ],

closes #1696

@lescai lescai added the docs label Oct 28, 2024
@lescai lescai self-assigned this Oct 28, 2024
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github-actions bot commented Oct 28, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit b282b15

+| ✅ 215 tests passed       |+
#| ❔  11 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2024-10-28 15:36:03

@lescai lescai merged commit b862f0e into nf-core:dev Oct 29, 2024
37 checks passed
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@FriederikeHanssen FriederikeHanssen FriederikeHanssen approved these changes

@maxulysse maxulysse Awaiting requested review from maxulysse maxulysse is a code owner

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@lescai @FriederikeHanssen