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Important! Template update for nf-core/tools v2.10 #1078

Merged
merged 3 commits into from
Oct 12, 2023
Merged

Important! Template update for nf-core/tools v2.10 #1078

merged 3 commits into from
Oct 12, 2023

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nf-core-bot
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Version 2.10 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-2.10 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 v2.10 release page.

@adamrtalbot adamrtalbot mentioned this pull request Oct 10, 2023
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github-actions bot commented Oct 11, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit ab55d1c

+| ✅ 145 tests passed       |+
#| ❔   6 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:

  • 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
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/rnaseq/rnaseq/.github/workflows/awstest.yml
  • multiqc_config - multiqc_config

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-10-11 20:03:29

maxulysse
maxulysse reviewed Oct 12, 2023
View reviewed changes
assets/multiqc_config.yml
@@ -1,7 +1,7 @@
report_comment: >
This report has been generated by the <a href="https://github.com/nf-core/rnaseq" target="_blank">nf-core/rnaseq</a>
This report has been generated by the <a href="https://github.com/nf-core/rnaseq/releases/tag/dev" target="_blank">nf-core/rnaseq</a>
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yeah this is wrong in the template too, we have no releases for dev

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Yep, agree. We need to find a way to fix this or just remove it. Will keep it in for now as it will break linting.

@drpatelh drpatelh merged commit 6ef512e into dev Oct 12, 2023
26 checks passed
@drpatelh drpatelh deleted the nf-core-template-merge-2.10 branch January 21, 2024 09:38
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@drpatelh drpatelh drpatelh left review comments

@maxulysse maxulysse maxulysse approved these changes

@adamrtalbot adamrtalbot Awaiting requested review from adamrtalbot

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@nf-core-bot @maxulysse @drpatelh