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Add happy container with rtgtools - #327

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georgiakes merged 8 commits into
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add-happy-rtgtools-image
Oct 1, 2026
Merged

Add happy container with rtgtools#327
georgiakes merged 8 commits into
devfrom
add-happy-rtgtools-image

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@georgiakes

@georgiakes georgiakes commented Sep 30, 2026

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PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/variantbenchmarking branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core pipelines lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

@github-actions

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

Posted for pipeline commit 92e3b67

+| ✅ 305 tests passed       |+
#| ❔   3 tests were ignored |#
#| ❔   1 tests had warnings |#
!| ❗   1 tests had warnings |!
Details

❗ Test warnings:

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: docs/images/nf-core-variantbenchmarking_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-variantbenchmarking_logo_dark.png
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore

❔ Tests fixed:

✅ Tests passed:

Run details

  • nf-core/tools version 4.1.0
  • Run at 2026-10-01 08:45:37

@github-actions

github-actions Bot commented Sep 30, 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 5/7

See the full run for details.

kubranarci
kubranarci reviewed Sep 30, 2026
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Comment thread conf/modules.config
withName: "HAPPY_HAPPY" {
ext.prefix = {params.truth_id ? "${meta.id}.${params.truth_id}.${meta.caller}" : "${meta.id}.truth.${meta.caller}" }
//ext.args = {""}
ext.args = { params.happy_comparison_engine != "default" ? "--engine=${params.happy_comparison_engine}" : "" }

@kubranarci kubranarci Sep 30, 2026

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did you to try to run it with all engine options?

@kubranarci kubranarci Sep 30, 2026

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just to see everything runs smooth for happy + reppy

@georgiakes georgiakes Sep 30, 2026

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I tested only the default which it the xcmp and the vcfeval.

@kubranarci kubranarci Sep 30, 2026

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I think it is worth to check, as comparison_method uses happy_comparison_engine directly and in rep.py module you mention comparison module should be either "happy" or "vcfeval" https://github.com/nf-core/variantbenchmarking/blob/dev/modules/nf-core/happy/report/meta.yml

@georgiakes georgiakes Sep 30, 2026

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I get issues related to the happy code that have been unanswered form 2023 https://github.com/Illumina/hap.py/issues/181

@kubranarci kubranarci Oct 1, 2026

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This seems like a formatting issue

@kubranarci kubranarci Oct 1, 2026

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I think the solution could be excluding those enginees for the pipeline and we can link the reasoning as this github issue.

Comment thread nextflow_schema.json Outdated
kubranarci
kubranarci reviewed Sep 30, 2026
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Comment thread conf/tests/test_ga4gh.config
@georgiakes
georgiakes merged commit e44e239 into dev Oct 1, 2026
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