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Important! Template update for nf-core/tools v2.14.0 #10

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wants to merge 3 commits into from
Closed

Important! Template update for nf-core/tools v2.14.0 #10

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nf-core-bot
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Version 2.14.0 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-2.14.0 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 v2.14.0 release page.

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github-actions bot commented May 9, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 85a3423

+| ✅ 198 tests passed       |+
#| ❔   7 tests were ignored |#
!| ❗  14 tests had warnings |!

❗ Test warnings:

  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
  • pipeline_todos - TODO string in README.md: Add bibliography of tools and data used in your pipeline
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
  • pipeline_todos - TODO string in output.md: Write this documentation describing your workflow's output
  • pipeline_todos - TODO string in ci.yml: You can customise CI pipeline run tests as required
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in main.nf: A stub section should mimic the execution of the original module as best as possible
  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • 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
  • nfcore_yml - nf-core version not set in .nf-core.yml

❔ Tests ignored:

  • template_strings - Ignoring Jinja template strings in file /home/runner/work/tfactivity/tfactivity/modules/local/report/create/app/templates/base.html
  • template_strings - Ignoring Jinja template strings in file /home/runner/work/tfactivity/tfactivity/modules/local/report/create/app/templates/configuration.html
  • template_strings - Ignoring Jinja template strings in file /home/runner/work/tfactivity/tfactivity/modules/local/report/create/app/templates/macros.html
  • template_strings - Ignoring Jinja template strings in file /home/runner/work/tfactivity/tfactivity/modules/local/report/create/app/templates/network.html
  • template_strings - Ignoring Jinja template strings in file /home/runner/work/tfactivity/tfactivity/modules/local/report/create/app/templates/snp.html
  • template_strings - Ignoring Jinja template strings in file /home/runner/work/tfactivity/tfactivity/modules/local/report/create/app/templates/tf.html
  • template_strings - Ignoring Jinja template strings in file /home/runner/work/tfactivity/tfactivity/modules/local/report/create/app/templates/tg.html

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.0
  • Run at 2024-05-09 07:35:49

@nictru
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nictru commented May 11, 2024

Closed due to hotfix 2.14.1 in #11

@nictru nictru closed this May 11, 2024
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