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feat: Add cadd for indels#59

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kristinebilgrav merged 31 commits into
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add-cadd
Apr 23, 2026
Merged

feat: Add cadd for indels#59
kristinebilgrav merged 31 commits into
devfrom
add-cadd

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@kristinebilgrav kristinebilgrav commented Mar 27, 2026 •
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Closes https://github.com/Clinical-Genomics/wgs-cancer-pipeline/issues/27

Added

  • CADD score annotation for indels
    • created a subworkflow for the process (annotate_cadd)
      • Only runs if the val_cadd_resources is populated
    • added modules GAWK, CADD and TABIX
    • compatibility with both GRCh37 and GRCh38 (although only tested with proper data and resources for GRCh38 - see issue for more details)
  • test for subworkflow:
    • NOTE: cadd resources are very large, which makes creating a test dataset hard, but this is being worked on in raredisease Add annotate_cadd subworkflow test nf-core/raredisease#794. We can update the test when this is completed. Therefore:
      • the subworkflow test is run in stub mode only currently
      • the default test does not run the annotate_cadd subworkflow

Test on hasta

  • The test for GRCh38 was successful (see issue for more details)
  • The test for GRCh37 was not run due to lack of resources.

@kristinebilgrav kristinebilgrav requested a review from a team as a code owner March 27, 2026 15:20
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github-actions Bot commented Mar 27, 2026

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 27, 2026 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit eab435a

+| ✅ 176 tests passed       |+
#| ❔  16 tests were ignored |#
!| ❗  14 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: Include a figure that guides the user through the major workflow steps. Many nf-core
  • 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 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 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.

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.5.2
  • Run at 2026-04-23 07:28:20

kristinebilgrav
kristinebilgrav commented Mar 27, 2026
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@kristinebilgrav kristinebilgrav marked this pull request as draft March 27, 2026 15:33
kristinebilgrav
kristinebilgrav commented Mar 30, 2026
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kristinebilgrav
kristinebilgrav commented Apr 13, 2026
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Comment thread subworkflows/local/annotate_cadd/tests/main.nf.test
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kristinebilgrav commented Apr 13, 2026
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Comment thread subworkflows/local/annotate_cadd/main.nf
@kristinebilgrav kristinebilgrav marked this pull request as ready for review April 14, 2026 13:19
beatrizsavinhas
beatrizsavinhas requested changes Apr 16, 2026
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@beatrizsavinhas beatrizsavinhas left a comment •
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I have quite a few comments and suggestions for changes, but for now the most important is to update the branch to the latest version of dev which should change this PR quite a bit.

Comment thread workflows/oncorefiner.nf Outdated
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Comment thread subworkflows/local/annotate_cadd/tests/nextflow.config
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Comment thread conf/subworkflows/annotate_cadd.config
Comment thread conf/test.config
@kristinebilgrav kristinebilgrav requested review from a team and beatrizsavinhas April 20, 2026 11:45
beatrizsavinhas
beatrizsavinhas approved these changes Apr 20, 2026
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Super nice additions to the tests! I left some minor comments and suggestions. But otherwise it looks good! 🌟

Comment thread conf/subworkflows/annotate_cadd.config
Comment thread subworkflows/local/annotate_cadd/tests/main.nf.test.snap
Comment thread subworkflows/local/utils_nfcore_oncorefiner_pipeline/main.nf Outdated
Comment thread subworkflows/local/utils_nfcore_oncorefiner_pipeline/main.nf
Comment thread CHANGELOG.md Outdated
Comment thread nextflow.config Outdated
Comment thread subworkflows/local/process_snvs/tests/main.nf.test
Comment thread subworkflows/local/annotate_cadd/main.nf Outdated
Comment thread subworkflows/local/annotate_cadd/main.nf Outdated
fellen31
fellen31 reviewed Apr 20, 2026
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@kristinebilgrav kristinebilgrav merged commit 7422634 into dev Apr 23, 2026
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@kristinebilgrav kristinebilgrav deleted the add-cadd branch April 23, 2026 07:34
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@beatrizsavinhas beatrizsavinhas beatrizsavinhas approved these changes

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@kristinebilgrav @beatrizsavinhas @fellen31