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Fix issue 719: Allow bait padding zero #757

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Merged
peterpru merged 3 commits into from
Dec 15, 2025
Merged

Fix issue 719: Allow bait padding zero #757

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3fcffb5
allow bait padding 0
peterpru Dec 12, 2025
03af0c5
add changelog
peterpru Dec 12, 2025
286db43
Merge branch 'dev' into allow-bait-padding-zero
ramprasadn Dec 15, 2025
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -27,6 +27,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- Fixed conda declaration in the add_varcallername_to_bed module [#733](https://github.com/nf-core/raredisease/pull/733)
- Fixed CADD annotation to support chr prefix [#745](https://github.com/nf-core/raredisease/pull/745)
- Fixed mismatch between VCF and ROH calls when analysing multiple samples [#755](https://github.com/nf-core/raredisease/pull/755)
- Fixed pipeline to run variant calling even with bait_padding set to 0 [#757](https://github.com/nf-core/raredisease/pull/757)

### Parameters

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2 changes: 1 addition & 1 deletion conf/modules/prepare_references.config
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Expand Up @@ -105,7 +105,7 @@ process {
}

withName: '.*PREPARE_REFERENCES:BEDTOOLS_PAD_TARGET_BED' {
ext.when = { params.target_bed && params.bait_padding > 0 }
ext.when = { params.target_bed }
ext.prefix = { "${meta.id}_pad${params.bait_padding}" }
ext.args = { "-b ${params.bait_padding}" }
}
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