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nf-core modules update -a#633

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maxulysse merged 22 commits intonf-core:devfrom
maxulysse:dev_modules_update
Jul 17, 2022
Merged

nf-core modules update -a#633
maxulysse merged 22 commits intonf-core:devfrom
maxulysse:dev_modules_update

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@maxulysse maxulysse commented Jul 14, 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 - 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 14, 2022 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 3e7bdd8

+| ✅ 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 2022-07-17 16:29:57

maxulysse
maxulysse commented Jul 14, 2022
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Comment thread CHANGELOG.md
FriederikeHanssen
FriederikeHanssen reviewed Jul 14, 2022
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Comment thread modules/nf-core/modules/samtools/stats/main.nf Outdated
FriederikeHanssen
FriederikeHanssen approved these changes Jul 14, 2022
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@FriederikeHanssen FriederikeHanssen left a comment

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looks good to me, a bit unhappy about the samtools stats module, but that is not this PR's concern

FriederikeHanssen
FriederikeHanssen approved these changes Jul 17, 2022
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Comment thread conf/modules.config
Comment thread conf/modules.config Outdated
FriederikeHanssen
FriederikeHanssen reviewed Jul 17, 2022
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Comment thread conf/modules.config
@maxulysse maxulysse merged commit 5b83a5d into nf-core:dev Jul 17, 2022
@maxulysse maxulysse deleted the dev_modules_update branch July 17, 2022 17:16
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@FriederikeHanssen FriederikeHanssen FriederikeHanssen approved these changes

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