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DRAFT: Extending output from snpEff#639

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FriederikeHanssen merged 4 commits intonf-core:devfrom
asp8200:extend_output_from_snpeff
Jul 16, 2022
Merged

DRAFT: Extending output from snpEff#639
FriederikeHanssen merged 4 commits intonf-core:devfrom
asp8200:extend_output_from_snpeff

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@asp8200 asp8200 commented Jul 16, 2022 •
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The purpose of this PR is just to include a summary-html-file and a genes-txt-file in the published output from snpEff.

Tests and git_sha of snpeff in modules.json have been updated.

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).

FriederikeHanssen
FriederikeHanssen reviewed Jul 16, 2022
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FriederikeHanssen commented Jul 16, 2022

looks good only thing missing is updating the module in nf-core/modules :)

asp8200 and others added 2 commits July 16, 2022 13:23
@asp8200 @FriederikeHanssen
Update conf/modules.config
31ad062 
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
@asp8200
Updating git_sha for snpEff
1552dfd
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github-actions Bot commented Jul 16, 2022 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 1552dfd

+| ✅ 145 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   1 tests had warnings |!
Details

❗ Test warnings:

  • readme - README did not have a Nextflow minimum version badge.

❔ 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 2022-07-16 18:25:22

@FriederikeHanssen FriederikeHanssen marked this pull request as ready for review July 16, 2022 19:37
@FriederikeHanssen FriederikeHanssen merged commit 3138184 into nf-core:dev Jul 16, 2022
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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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