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feat: Add Tumor only and Tumor Normal tests#69

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add-to-and-tn-tests
Open

feat: Add Tumor only and Tumor Normal tests#69
beatrizsavinhas wants to merge 6 commits intodevfrom
add-to-and-tn-tests

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@beatrizsavinhas beatrizsavinhas commented Apr 7, 2026 •
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Closes https://github.com/Clinical-Genomics/CancerBioInfo/issues/118.

Added

  • tumor_only.nf.test and snapshot.

Changed

  • Renamed default test to tumor_normal.nf.test and updated snapshot.
  • Added default test to lint ignore to prevent linting errors.

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github-actions bot commented Apr 7, 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 or added code that should be tested, add tests!
  • If you've added a new tool, follow the pipeline conventions in the Contributing Guidelines.
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

@beatrizsavinhas beatrizsavinhas changed the title Renamed default test to tumor_normal Add Tumor only and Tumor Normal tests Apr 7, 2026
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github-actions bot commented Apr 7, 2026 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit b058d81

+| ✅ 183 tests passed       |+
#| ❔  16 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: 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 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!
  • 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
  • local_component_structure - prepare_references.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.5.2
  • Run at 2026-04-07 09:06:47

@beatrizsavinhas beatrizsavinhas changed the title Add Tumor only and Tumor Normal tests feat: Add Tumor only and Tumor Normal tests Apr 7, 2026
@beatrizsavinhas beatrizsavinhas marked this pull request as ready for review April 7, 2026 09:05
@beatrizsavinhas beatrizsavinhas requested a review from a team as a code owner April 7, 2026 09:05
fevac
fevac reviewed Apr 7, 2026
View reviewed changes
tests/tumor_only.nf.test
Comment on lines +11 to +13
outdir = "$outputDir"
bam_normal = null
bai_normal = null
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@fevac fevac Apr 7, 2026

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vcf files should also be different for tumor only test. TN vcf files will have information for two samples (two columns), while TO only one. We could modify the current vcf files to mimic TO mode. However it would be best to to re-run the test data in tumor only mode to make sure we test with real OA output files (there are differences in how OA runs when in TO vs TN).

I would argue for having a dedicated profile for TO separated from TN

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@beatrizsavinhas beatrizsavinhas Apr 7, 2026

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Yeah, I had also thought of doing separate TO and TN configs but then I also thought it would be nice to have a default test config so you can run the usual commands nextflow run -profile test etc.
Perhaps we could just include the TN config in conf/test.config? What do you think of that solution?

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@beatrizsavinhas beatrizsavinhas Apr 7, 2026

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I also agree that it's best to re-run the test data through oncoanalyser in tumor only mode!

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Yeah, I had also thought of doing separate TO and TN configs but then I also thought it would be nice to have a default test config so you can run the usual commands nextflow run -profile test etc. Perhaps we could just include the TN config in conf/test.config? What do you think of that solution?

Yes, I like that. Also TN should be the "standard/default", and TO the "special case"

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