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feat: Add shared config logic - #13

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beatrizsavinhas wants to merge 9 commits into
add-cascadefrom
add-config-logic
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feat: Add shared config logic#13
beatrizsavinhas wants to merge 9 commits into
add-cascadefrom
add-config-logic

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@beatrizsavinhas

@beatrizsavinhas beatrizsavinhas commented Jul 9, 2026 •
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This change allows for providing only 1 config file to oncoflow which is then automatically propagated to all included pipelines.

Changed

  • Logic to propagate the oncoflow config file for all run pipelines.

Removed

  • oncoanalyser_config and oncoanalyser_config input parameters.

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github-actions Bot commented Jul 9, 2026 •
edited by beatrizsavinhas
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PR checklist

  • Fill in description of the PR and link to any relevant issues.
  • If you've fixed a bug, added a subworkflow or any other code that should be tested, add tests!
  • If you've added a new tool, update citations according to the instructions under Adding Citations.
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • README.md is updated (including authors/contributors).

See Contributing Guidelines for more details on how to contribute according to pipeline conventions.

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github-actions Bot commented Jul 9, 2026 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 66128e4

+| ✅ 161 tests passed       |+
#| ❔  27 tests were ignored |#
!| ❗  22 tests had warnings |!
Details

❗ Test warnings:

  • files_exist - File not found: assets/multiqc_config.yml
  • 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 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 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 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 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.
  • schema_lint - Parameter input not found in schema

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 4.0.2
  • Run at 2026-07-10 10:39:12

@beatrizsavinhas
beatrizsavinhas changed the base branch from dev to add-cascade July 10, 2026 06:56
@beatrizsavinhas

beatrizsavinhas commented Jul 10, 2026

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To do:

Add logic to test these changes.

@beatrizsavinhas beatrizsavinhas mentioned this pull request Jul 10, 2026
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