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Update all the modules#734

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maxulysse merged 27 commits intonf-core:devfrom
maxulysse:dev_modules_update
Sep 8, 2022
Merged

Update all the modules#734
maxulysse merged 27 commits intonf-core:devfrom
maxulysse:dev_modules_update

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@maxulysse maxulysse commented Sep 7, 2022

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).

@maxulysse maxulysse marked this pull request as draft September 7, 2022 10:07
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github-actions bot commented Sep 7, 2022 •
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nf-core lint overall result: Passed ✅

Posted for pipeline commit 805cc1d

+| ✅ 151 tests passed       |+
#| ❔   4 tests were ignored |#
Details

❔ 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 2022-09-07 16:21:54

@FriederikeHanssen
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FriederikeHanssen commented Sep 7, 2022

samtools also had a new release.. should we bump?

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FriederikeHanssen commented Sep 7, 2022

the md cram update, I can do in a separate PR, because it needs some adaption to the subworkflows

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maxulysse commented Sep 7, 2022

samtools also had a new release.. should we bump?

Good idea

the md cram update, I can do in a separate PR, because it needs some adaption to the subworkflows

Forgot about it, that's a good idea indeed, let me revert that one

@FriederikeHanssen FriederikeHanssen mentioned this pull request Sep 7, 2022
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@maxulysse maxulysse marked this pull request as ready for review September 7, 2022 15:14
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FriederikeHanssen approved these changes Sep 7, 2022
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❤️

@maxulysse maxulysse merged commit f7c4caf into nf-core:dev Sep 8, 2022
@maxulysse maxulysse deleted the dev_modules_update branch September 8, 2022 06:59
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