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add docs for bcftools annotate params #1335

Merged
merged 11 commits into from
Nov 20, 2023
Merged

add docs for bcftools annotate params #1335

merged 11 commits into from
Nov 20, 2023

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FriederikeHanssen
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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/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).

@FriederikeHanssen
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adding some validation as well...

@FriederikeHanssen FriederikeHanssen marked this pull request as draft November 16, 2023 10:28
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github-actions bot commented Nov 16, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit fa45aab

+| ✅ 144 tests passed       |+
#| ❔   9 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in WorkflowSarek.groovy: Optionally add in-text citation tools to this list.

❔ 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 2023-11-20 07:46:30

@FriederikeHanssen FriederikeHanssen marked this pull request as ready for review November 16, 2023 10:34
@FriederikeHanssen
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@nf-core-bot fix linting

nf-core-bot and others added 3 commits November 16, 2023 11:16
@nf-core-bot
[automated] Fix linting with Prettier
a815fda
@FriederikeHanssen
fix brackets
70d52c8
@FriederikeHanssen @maxulysse
Update CHANGELOG.md
8f34778 
Co-authored-by: Maxime U Garcia <maxime.garcia@scilifelab.se>
@FriederikeHanssen
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@nf-core-bot fix linting

maxulysse
maxulysse reviewed Nov 16, 2023
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nextflow_schema.json Outdated Show resolved Hide resolved
@FriederikeHanssen
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@nf-core-bot fix linting

@maxulysse
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failing tests are just the sention ones, so ok to merge

@FriederikeHanssen FriederikeHanssen merged commit 7f114f7 into nf-core:dev Nov 20, 2023
22 of 27 checks passed
@FriederikeHanssen FriederikeHanssen deleted the fix_annotate_docs branch November 20, 2023 08:14
@maxulysse maxulysse mentioned this pull request Dec 8, 2023
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@grantn5 grantn5 grantn5 left review comments

@maxulysse maxulysse maxulysse approved these changes

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@FriederikeHanssen @maxulysse @grantn5 @nf-core-bot