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sync 2.5 #720

Merged
merged 13 commits into from
Sep 2, 2022
Merged

sync 2.5 #720

merged 13 commits into from
Sep 2, 2022

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maxulysse
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Replace and close #718

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 Aug 30, 2022 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 641e2c7

+| ✅ 149 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

❔ 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 2.5.1
  • Run at 2022-09-02 08:17:40

@FriederikeHanssen
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Changelog?

@maxulysse
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controlfreec tests are working locally, no idea what is actually the issue there...

@FriederikeHanssen
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maybe its mpileup it also fails

@maxulysse
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Removed the md5sum related to mpileup, I'll see what happens with controlfreec

maxulysse
maxulysse commented Sep 1, 2022
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maxulysse
maxulysse commented Sep 1, 2022
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maxulysse
maxulysse commented Sep 1, 2022
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maxulysse
maxulysse commented Sep 1, 2022
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@maxulysse maxulysse mentioned this pull request Sep 1, 2022
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@maxulysse maxulysse merged commit 60d5aa1 into nf-core:dev Sep 2, 2022
@maxulysse maxulysse deleted the dev_sync_2.5 branch September 5, 2022 12:24
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@FriederikeHanssen FriederikeHanssen FriederikeHanssen approved these changes

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@maxulysse @FriederikeHanssen @nf-core-bot