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161 cnv benchmark subworkflow #163

Merged
merged 10 commits into from
Mar 7, 2025
Merged

161 cnv benchmark subworkflow #163

merged 10 commits into from
Mar 7, 2025

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kubranarci
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  • new analysis type especially for CNV benchmarking. Enables intersection of BED regions using bedtools.
  • truvari works for cnv benchmarking only if pctseq = 0 --> means no sequence resolve needed.
  • new test case for cnv benchmarking and snapshots
  • intersect added to the metromap
  • intersection will be possible my target_regions input, if not provided VCF can be converted to BED for intersection analysis.

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).

@kubranarci kubranarci linked an issue Mar 6, 2025 that may be closed by this pull request
fix broken link describing truth sets #156
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nvnieuwk
nvnieuwk reviewed Mar 6, 2025
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nvnieuwk
nvnieuwk reviewed Mar 6, 2025
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subworkflows/local/intersect_statistics/main.nf
Comment on lines +19 to +25
test.branch{
def vcf_file = it[1]
def regions_file = it[2]
vcf : vcf_file
regions : regions_file
other: false}
.set{test_samples}
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What's this layout? 😁

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I have two types of inputs, one is vcf the other is regions bed file. This stream should branch them accordingly. First check assures if vcf file is given, second is to check if regions exist :D it is a bit messy I know. But let me know if you have something better on your mind

nvnieuwk
nvnieuwk approved these changes Mar 6, 2025
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Some minor comments, you can merge this in once you've addressed these :)

@kubranarci kubranarci merged commit 2d2773f into dev Mar 7, 2025
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@kubranarci kubranarci deleted the 161-cnv-benchmark-subworkflow branch March 7, 2025 10:18
@kubranarci kubranarci linked an issue Mar 7, 2025 that may be closed by this pull request
CNV benchmark subworkflow #161
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@nvnieuwk nvnieuwk nvnieuwk approved these changes

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CNV benchmark subworkflow fix broken link describing truth sets
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@kubranarci @nvnieuwk