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Important! Template update for nf-core/tools v2.12 #9

Merged
merged 12 commits into from
Feb 2, 2024
Merged

Important! Template update for nf-core/tools v2.12 #9

merged 12 commits into from
Feb 2, 2024

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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 Jan 29, 2024 •
edited

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit f3081eb

+| ✅ 188 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗  19 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: TODO nf-core:
  • pipeline_todos - TODO string in README.md: Include a figure that guides the user through the major workflow steps. Many nf-core
  • pipeline_todos - TODO string in README.md: Fill in short bullet-pointed list of the default steps in the pipeline
  • pipeline_todos - TODO string in README.md: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
  • pipeline_todos - TODO string in README.md: update the following command to include all required parameters for a minimal example
  • pipeline_todos - TODO string in README.md: If applicable, make list of people who have also contributed
  • 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 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 output.md: Write this documentation describing your workflow's output
  • pipeline_todos - TODO string in usage.md: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website.
  • pipeline_todos - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
  • pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed
  • 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 WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
  • pipeline_todos - TODO string in WorkflowRiboseq.groovy: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.12.1
  • Run at 2024-02-02 10:56:00

@pinin4fjords pinin4fjords merged commit ca556ad into dev Feb 2, 2024
51 checks passed
@pinin4fjords pinin4fjords deleted the nf-core-template-merge-2.12 branch February 2, 2024 10:55
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@pinin4fjords pinin4fjords pinin4fjords approved these changes

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