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feat: Add subworkflow generate_cytosure_files#60

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beatrizsavinhas merged 80 commits intodevfrom
add-vcf2cytosure
Apr 13, 2026
Merged

feat: Add subworkflow generate_cytosure_files#60
beatrizsavinhas merged 80 commits intodevfrom
add-vcf2cytosure

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@beatrizsavinhas beatrizsavinhas commented Mar 30, 2026 •
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Closes https://github.com/Clinical-Genomics/CancerBioInfo/issues/102.

Added

  • TIDDIT_COV from nf-core/modules.

  • VCF2CYTOSURE from nf-core/modules.

  • Subworkflow GENERATE_CYTOSURE_FILES.

    • Input:

      • SV VCF file given in the parameters.
      • SV VCF .tbi file.
      • ch_bam_bai for tumor and (optionally) normal sample.

    • Steps:

      • FILTER_VCF using BCFTOOLS_VIEW to filter out SGL variants from input sv_vcf.
      • TIDDIT_COV to generate coverage bed file, for tumor and (optionally) normal sample.
      • VCF2CYTOSURE to generate .cgh file for tumor and (optionally) normal sample.

    • Config: conf/subworkflows/generate_cytosure_files.config.

    • Test with tumor sample.

    • Test snapshot.

Changed

  • Added ch_bam_bai_normal and ch_bam_bai_tumor to input of ONCOREFINER for downstream use by GENERATE_CYTOSURE_FILES.
  • Updated default test snapshot to include new .cgh files.

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github-actions Bot commented Mar 30, 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 contribution docs.
  • 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).

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github-actions Bot commented Mar 30, 2026 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit b6020d7

+| ✅ 181 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: 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 nextflow.config: Specify any additional parameters here
  • 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 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.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 base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
  • 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 2026-04-10 10:25:55

@beatrizsavinhas beatrizsavinhas changed the title Add vcf2cytosure feat: Add vcf2cytosure Mar 30, 2026
@beatrizsavinhas beatrizsavinhas marked this pull request as ready for review April 2, 2026 15:42
@beatrizsavinhas beatrizsavinhas requested a review from a team as a code owner April 2, 2026 15:42
kristinebilgrav
kristinebilgrav reviewed Apr 7, 2026
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Comment thread subworkflows/local/generate_cytosure_files/main.nf
kristinebilgrav
kristinebilgrav reviewed Apr 7, 2026
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Comment thread tests/default.nf.test.snap
fevac
fevac approved these changes Apr 8, 2026
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This looks great! Thanks 🌟

Comment thread subworkflows/local/generate_cytosure_files/tests/main.nf.test Outdated
Comment thread subworkflows/local/generate_cytosure_files/tests/main.nf.test.snap Outdated
kristinebilgrav
kristinebilgrav reviewed Apr 10, 2026
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Looks great! 🚀

kristinebilgrav
kristinebilgrav reviewed Apr 10, 2026
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Comment thread subworkflows/local/generate_cytosure_files/tests/main.nf.test
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Looks great! 🌟

Comment thread subworkflows/local/generate_cytosure_files/tests/main.nf.test
Comment thread workflows/oncorefiner.nf
@beatrizsavinhas beatrizsavinhas merged commit 2eb99d2 into dev Apr 13, 2026
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@beatrizsavinhas beatrizsavinhas deleted the add-vcf2cytosure branch April 13, 2026 06:44
@beatrizsavinhas beatrizsavinhas mentioned this pull request Apr 21, 2026
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@kristinebilgrav kristinebilgrav kristinebilgrav approved these changes

@fevac fevac fevac approved these changes

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