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refactor: Update TEMPLATE branch#40

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beatrizsavinhas merged 7 commits intoTEMPLATEfrom
update-template
Mar 17, 2026
Merged

refactor: Update TEMPLATE branch#40
beatrizsavinhas merged 7 commits intoTEMPLATEfrom
update-template

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@beatrizsavinhas beatrizsavinhas commented Mar 10, 2026 •
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Changed

  • Updates .nf-core.yml according to latest changes in dev.
  • Updated template with nf-core pipelines sync.
  • Generate default test snapshot with nf-test test . --profile=+docker --update-snapshot.

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github-actions bot commented Mar 10, 2026 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 634bcc9

+| ✅ 167 tests passed       |+
#| ❔  14 tests were ignored |#
!| ❗  25 tests had warnings |!
Details

❗ 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 2. Present QC for raw reads (MultiQC)
  • 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 nextflow.config: Specify your pipeline's command line flags
  • pipeline_todos - TODO string in nextflow.config: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
  • pipeline_todos - TODO string in nextflow.config: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0
  • 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 nextflow.config: Specify any additional parameters here
  • 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 output.md: Write this documentation describing your workflow's output
  • 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 test.config: Specify the paths to your test data on nf-core/test-datasets
  • pipeline_todos - TODO string in test.config: Give any required params for the test so that command line flags are not needed
  • 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 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!

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.5.2
  • Run at 2026-03-10 13:09:48

@beatrizsavinhas beatrizsavinhas self-assigned this Mar 10, 2026
@beatrizsavinhas beatrizsavinhas changed the title Update TEMPLATE branch refactor: Update TEMPLATE branch Mar 10, 2026
fevac
fevac approved these changes Mar 12, 2026
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Thanks for updating this! 💪 I didn't see anything that I could react to but I'm very new to these templates updates

@beatrizsavinhas beatrizsavinhas merged commit aeb1223 into TEMPLATE Mar 17, 2026
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@beatrizsavinhas beatrizsavinhas deleted the update-template branch March 17, 2026 12:04
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