8000 Identified a WES ASCAT Error and updated documentation by alexanderchang1 · Pull Request #1638 · nf-core/sarek · GitHub
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Identified a WES ASCAT Error and updated documentation #1638

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Merged
merged 6 commits into from
Dec 10, 2024
Merged

Identified a WES ASCAT Error and updated documentation #1638

merged 6 commits into from
Dec 10, 2024

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alexanderchang1
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PR checklist

  • This comment contains a description of changes (with reason).
  • Usage Documentation in docs/usage.md is updated.

This is solely a documentation change in the usage.md file that allows using WES references provided by ASCAT, it's more user friendly than the currently recommended Battenberg method and also avoids a null-pointer error when running prepare.hts for ASCAT.

@alexanderchang1
Update usage.md
8aa4c53 
Made changes that document usage of WES references from the ASCAT developers and how to avoid a null pointer error
@alexanderchang1
Merge pull request #1 from alexanderchang1/alexanderchang1-patch-WES-…
873d9d8 
…ascat

Update usage.md
@maxulysse
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Can you update the CHANGELOG.md file?

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@nf-core-bot fix linting pretty please 🙏

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github-actions bot commented Sep 2, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 5415caa

+| ✅ 201 tests passed       |+
#| ❔  12 tests were ignored |#
!| ❗   3 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!

❔ Tests ignored:

  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • files_exist - File is ignored: .github/workflows/awstest.yml
  • files_exist - File is ignored: conf/modules.config
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: assets/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_dark.png
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore
  • actions_ci - actions_ci
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/sarek/sarek/.github/workflows/awstest.yml
  • template_strings - template_strings
  • modules_config - modules_config

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-10-04 08:21:49

@alexanderchang1 alexanderchang1 mentioned this pull request Sep 2, 2024
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@alexanderchang1
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alexanderchang1 commented Sep 2, 2024 •
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Added the changelog pull request in #1641

EDIT: Closed that PR, didn't notice that commit for changelog was already included here. Changelog has been edited.

FriederikeHanssen
FriederikeHanssen approved these changes Dec 10, 2024
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Thanks a lot!

@FriederikeHanssen FriederikeHanssen merged commit abdea49 into nf-core:dev Dec 10, 2024
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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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