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Fixing the bug: target_bed was missing in liftover - #320

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kubranarci merged 7 commits into
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312-lifting-over-regions-and-targets-bed-is-missing
Aug 19, 2026
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Fixing the bug: target_bed was missing in liftover#320
kubranarci merged 7 commits into
devfrom
312-lifting-over-regions-and-targets-bed-is-missing

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@kubranarci

@kubranarci kubranarci commented Aug 17, 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).

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github-actions Bot commented Aug 17, 2026

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Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 4.0.3.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the Synchronisation documentation.

@kubranarci

kubranarci commented Aug 17, 2026

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@nf-core-bot fix linting

@github-actions

github-actions Bot commented Aug 17, 2026 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 793495b

+| ✅ 302 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   2 tests had warnings |!
Details

❗ Test warnings:

  • schema_lint - Schema 'description' should be 'Variant Benchmarking pipeline for germline and somatic variant callers '
    Found: 'Variant Benchmarking pipeline for germline and somatic variant callers'
  • schema_lint - Input mimetype is missing or empty

❔ 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 passed:

Run details

  • nf-core/tools version 4.0.3
  • Run at 2026-08-19 11:47:49

@kubranarci

kubranarci commented Aug 18, 2026

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@nf-core-bot fix linting

@github-actions

github-actions Bot commented Aug 18, 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 6/7

See the full run for details.

@kubranarci

kubranarci commented Aug 19, 2026

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@khersameesh24 can you. maybe review this?

khersameesh24
khersameesh24 reviewed Aug 19, 2026
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Comment thread subworkflows/local/liftover_vcfs/main.nf Outdated
// liftover high confidence bed file if given
// liftover bed files if given
ch_targets_bed.map{file -> tuple([id: "targets"], file)}
.mix(ch_bed.map{file -> tuple([id: "regions"], file)})

@khersameesh24 khersameesh24 Aug 19, 2026

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Hi @kubranarci , this is a minor issue but I think file is a keyword in nextflow, maybe you can name the variable something else. This mostly works but might have unexpected behavior and would be hard to debug later. I think it also highlights the file variable in different color because it is a reserved keyword

@kubranarci kubranarci Aug 19, 2026

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I see, thanks you! I will change it.

khersameesh24
khersameesh24 approved these changes Aug 19, 2026
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@kubranarci, looks good, just a minor comment

@kubranarci

kubranarci commented Aug 19, 2026

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@nf-core-bot fix linting

@kubranarci
kubranarci merged commit fbe7140 into dev Aug 19, 2026
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@kubranarci
kubranarci deleted the 312-lifting-over-regions-and-targets-bed-is-missing branch August 19, 2026 12:02
@kubranarci kubranarci linked an issue Aug 19, 2026 that may be closed by this pull request
lifting over regions and targets bed is missing #312
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lifting over regions and targets bed is missing

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