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feat: Add unique run name configuration to ensure compatibility with Tower - #20

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feat: Add unique run name configuration to ensure compatibility with Tower#20
beatrizsavinhas wants to merge 6 commits into
devfrom
add-tower-configuration

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@beatrizsavinhas

@beatrizsavinhas beatrizsavinhas commented Sep 2, 2026 •
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Closes https://github.com/Clinical-Genomics/MTP-oncoflow/issues/140.

Added

Based on Clinical-Genomics/metaflow@cfb7cae:

  • Input parameter run_name to NEXTFLOW_RUN module.
  • Logic to provide unique run name -name ${run_name}_${timestamp} to nextflow run command in NEXTFLOW_RUN.
  • Logic to provide case_id as run_name for child pipelines.

Changed

Fixed

Removed

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github-actions Bot commented Sep 2, 2026

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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 Sep 2, 2026 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit c023e4a

+| ✅ 162 tests passed       |+
#| ❔  27 tests were ignored |#
!| ❗  24 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 CHANGELOG.md: ## v1.0.0dev - [unreleased replace with date on release ]
  • 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 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_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
  • schema_lint - Parameter input not found in schema

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 4.1.0
  • Run at 2026-09-03 07:52:37

@Clinical-Genomics Clinical-Genomics deleted a comment from github-actions Bot Sep 3, 2026
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github-actions Bot commented Sep 3, 2026 •
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❌ nf-test failed with latest Nextflow version

Note

Tests with Nextflow's latest version failed but it will not cause a CI workflow failure.
Please check if the failure is expected with newer (edge-)releases of Nextflow or if it needs fixing.

  • ❌ docker | latest-everything | Shard 2/2

See the full run for details.

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@beatrizsavinhas