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Important! Template update for nf-core/tools v2.12 #1201

Merged
merged 11 commits into from
Feb 5, 2024
Merged

Important! Template update for nf-core/tools v2.12 #1201

merged 11 commits into from
Feb 5, 2024

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nf-core-bot
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Version 2.12 of nf-core/tools has just been released with updates to the nf-core template. This automated pull-request attempts to apply the relevant updates to this pipeline.

Please make sure to merge this pull-request as soon as possible, resolving any merge conflicts in the nf-core-template-merge-2.12 branch (or your own fork, if you prefer). Once complete, make a new minor release of your pipeline.

For instructions on how to merge this PR, please see https://nf-co.re/docs/contributing/sync/.

For more information about this release of nf-core/tools, please see the v2.12 release page.

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github-actions bot commented Feb 4, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 4be91ac

+| ✅ 182 tests passed       |+
#| ❔   5 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: .github/workflows/awstest.yml
  • files_exist - File not found: .github/workflows/awsfulltest.yml
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • pipeline_todos - TODO string in WorkflowRnaseq.groovy: Optionally add in-text citation tools to this list.

❔ Tests ignored:

  • nextflow_config - Config default ignored: params.ribo_database_manifest
  • files_unchanged - File ignored due to lint config: assets/email_template.html
  • files_unchanged - File ignored due to lint config: assets/email_template.txt
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/rnaseq/rnaseq/.github/workflows/awstest.yml

✅ Tests passed:

Run details

  • nf-core/tools version 2.12.1
  • Run at 2024-02-05 10:13:53

@drpatelh drpatelh mentioned this pull request Feb 4, 2024
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drpatelh commented Feb 4, 2024

I have fixed the lint and pipeline tests locally but had to update all nf-core/modules and subworkflows. This will mean that over 200 files will be changed in if I push in this PR. Let me know if you want me to push the changes here @adamrtalbot or if you have another route.

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drpatelh commented Feb 5, 2024

@nf-core-bot fix linting

maxulysse
maxulysse reviewed Feb 5, 2024
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maxulysse
maxulysse approved these changes Feb 5, 2024
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I don't like the ch in the emit statements, I'll take that over in a maintainers meeting

@drpatelh @maxulysse
Update README.md
4be91ac 
Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>
@adamrtalbot adamrtalbot merged commit 07d7543 into dev Feb 5, 2024
27 checks passed
@adamrtalbot adamrtalbot deleted the nf-core-template-merge-2.12 branch February 5, 2024 11:06
@adamrtalbot adamrtalbot linked an issue Mar 11, 2024 that may be closed by this pull request
Update existing modules to recent versions including nf-test #1182
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@adamrtalbot adamrtalbot mentioned this pull request Mar 11, 2024
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@maxulysse maxulysse maxulysse approved these changes

@adamrtalbot adamrtalbot adamrtalbot approved these changes

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Update existing modules to recent versions including nf-test
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