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Use original QC values for Deepvariant after BQSR #1733

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Use original QC values for Deepvariant after BQSR #1733

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b1f75d1
use original qc values if BQSR was run before DV
FriederikeHanssen Nov 15, 2024
d709949
update changelog
FriederikeHanssen Nov 15, 2024
7bef573
use extra flag
FriederikeHanssen Nov 16, 2024
bbf7a9e
add nftest
FriederikeHanssen Nov 16, 2024
648a670
remove test profile
FriederikeHanssen Nov 16, 2024
7ae5034
adjust argument
FriederikeHanssen Nov 19, 2024
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -41,6 +41,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [1695](https://github.com/nf-core/sarek/pull/1695) - Fix and update input_schema.json
- [1702](https://github.com/nf-core/sarek/pull/1702) - Update nf-schema tests that were not failing on lenient mode
- [1712](https://github.com/nf-core/sarek/pull/1712) - Fix missing import statements on error messages when starting without samplesheet
- [1733](https://github.com/nf-core/sarek/pull/1733) - Use original quality values if DeepVariant is run on recalibrated data

### Removed

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5 changes: 4 additions & 1 deletion conf/modules/deepvariant.config
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Expand Up @@ -16,7 +16,10 @@
process {

withName: 'DEEPVARIANT_RUNDEEPVARIANT' {
ext.args = { params.wes ? "--model_type=WES" : "--model_type=WGS" }
ext.args = [
params.wes ? "--model_type=WES" : "--model_type=WGS" ,
!params.skip_tools.contains("baserecalibrator") ? "--parse_sam_aux_fields --use_original_quality_scores" : ''
].join(' ').trim()
ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.deepvariant" : "${meta.id}.deepvariant.${intervals.baseName}" }
ext.when = { params.tools && params.tools.split(',').contains('deepvariant') }
publishDir = [
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