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update vep and snpeff modules #632

Merged
merged 9 commits into from
Jul 13, 2022
Merged

update vep and snpeff modules #632

merged 9 commits into from
Jul 13, 2022

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maxulysse
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@maxulysse maxulysse commented Jul 13, 2022 •
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  • add snpeff_version params to better control container
  • add vep_include_fasta params to control usage of fasta file for annotation with VEP

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 - add to the software_versions process and a regex to scrape_software_versions.py
    • 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).
  • 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 Jul 13, 2022 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 3e70227

+| ✅ 145 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • readme - README did not have a Nextflow minimum version badge.
  • schema_description - No description provided in schema for parameter: ascat_chromosomes

❔ Tests ignored:

  • 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

✅ Tests passed:

Run details

  • nf-core/tools version 2.4.1
  • Run at 2022-07-13 14:37:24

lassefolkersen
lassefolkersen approved these changes Jul 13, 2022
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Looks good. very nice work

FriederikeHanssen
FriederikeHanssen approved these changes Jul 13, 2022
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minor comments on docs

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@maxulysse maxulysse merged commit 42b1860 into nf-core:dev Jul 13, 2022
@maxulysse maxulysse deleted the dev_annotation branch July 13, 2022 15:18
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@FriederikeHanssen FriederikeHanssen FriederikeHanssen approved these changes

@lassefolkersen lassefolkersen lassefolkersen approved these changes

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@maxulysse @lassefolkersen @FriederikeHanssen