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replace local subworkflow with nf-core version - vcf_annotate_ensemblvep #865

Merged
merged 16 commits into from
Nov 25, 2022
Merged

replace local subworkflow with nf-core version - vcf_annotate_ensemblvep #865

merged 16 commits into from
Nov 25, 2022

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maxulysse
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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).

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github-actions bot commented Nov 24, 2022 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit e9921ab

+| ✅ 151 tests passed       |+
#| ❔   8 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline
  • schema_description - No description provided in schema for parameter: cnvkit_reference

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.6
  • Run at 2022-11-25 17:10:49

@maxulysse
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@nf-core-bot fix linting pretty please 🙏

FriederikeHanssen
FriederikeHanssen reviewed Nov 25, 2022
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@FriederikeHanssen
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the annotate.conf probably needs someupdating too since we rely on the naming there

@maxulysse
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the annotate.conf probably needs someupdating too since we rely on the naming there

Was planning to do so in a coming commit

@maxulysse maxulysse merged commit ae76448 into nf-core:dev Nov 25, 2022
@maxulysse maxulysse deleted the dev_vcf_annotate_ensemblvep branch November 25, 2022 18:01
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@FriederikeHanssen FriederikeHanssen FriederikeHanssen left review comments

@matthdsm matthdsm matthdsm approved these changes

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@maxulysse @FriederikeHanssen @matthdsm @nf-core-bot