8000 Add bcftools annotate by grantn5 · Pull Request #1267 · nf-core/sarek · GitHub
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Merged
merged 19 commits into from
Oct 18, 2023
Merged

Add bcftools annotate #1267

merged 19 commits into from
Oct 18, 2023

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grantn5
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@grantn5 grantn5 commented Oct 2, 2023

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/sarek 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>).
  • 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).

@grantn5 grantn5 requested a review from maxulysse as a code owner October 2, 2023 16:31
FriederikeHanssen
FriederikeHanssen reviewed Oct 16, 2023
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FriederikeHanssen
FriederikeHanssen reviewed Oct 16, 2023
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github-actions bot commented Oct 16, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 33464b2

+| ✅ 144 tests passed       |+
#| ❔   9 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in WorkflowSarek.groovy: Optionally add in-text citation tools to this list.
  • schema_description - No description provided in schema for parameter: bcftools_annotations
  • schema_description - No description provided in schema for parameter: bcftools_annotations_index
  • schema_description - No description provided in schema for parameter: bcftools_header_lines

❔ Tests ignored:

  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • files_exist - File is ignored: conf/modules.config
  • 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: lib/NfcoreTemplate.groovy
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml
  • actions_ci - actions_ci
  • template_strings - template_strings

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-10-18 14:57:01

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grantn5 commented Oct 16, 2023

@FriederikeHanssen

maxulysse
maxulysse reviewed Oct 16, 2023
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maxulysse
maxulysse reviewed Oct 16, 2023
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maxulysse
maxulysse approved these changes Oct 18, 2023
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A couple of stuff that we could improve but not a problem for me

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Taking back my approval :D we need a test

@FriederikeHanssen FriederikeHanssen self-requested a review October 18, 2023 09:51
@grantn5 grantn5 merged commit 2336ae3 into nf-core:dev Oct 18, 2023
@grantn5 grantn5 deleted the add_bcftools_annotate branch October 18, 2023 16:10
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@maxulysse maxulysse maxulysse approved these changes

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

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