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1 change: 1 addition & 0 deletions CHANGELOG.md
Original file line number Diff line number Diff line change
Expand Up @@ -32,6 +32,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- Added constraints to block the pipeline from running CollectWgsMetrics on WES samples [#396](https://github.com/nf-core/raredisease/pull/396)
- Updated modules from nf-core [#412](https://github.com/nf-core/raredisease/pull/412)
- If present, remove duplicate entries in probands and upd_children in the meta. [#420](https://github.com/nf-core/raredisease/pull/420)
- Fixes vep starting as many instances as the square of the number of scatters. [#405](https://github.com/nf-core/raredisease/pull/405)

### `Updated`

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10 changes: 5 additions & 5 deletions subworkflows/local/annotate_snvs.nf
Original file line number Diff line number Diff line change
Expand Up @@ -102,12 +102,12 @@ workflow ANNOTATE_SNVS {

// If CADD is run, pick CADD output as input for VEP else pass selectvariants output to VEP.
GATK4_SELECTVARIANTS.out.vcf
.combine(ANNOTATE_CADD.out.vcf.ifEmpty("null")) // If CADD is not run then this channel will be empty, so assign a default value to allow filtering with branch operator
.branch { it -> // If CADD is run, then "it" will be [[meta],selvar.vcf,[meta],cadd.vcf], else [[meta],selvar.vcf,null]
selvar: it[2].equals("null")
.join(ANNOTATE_CADD.out.vcf, remainder: true) // If CADD is not run then the third element in this channel will be `null`
.branch { it -> // If CADD is run, then "it" will be [[meta],selvar.vcf,cadd.vcf], else [[meta],selvar.vcf,null]
selvar: it[2].equals(null)
return [it[0], it[1]]
cadd: !(it[2].equals("null"))
return [it[2], it[3]]
cadd: !(it[2].equals(null))
return [it[0], it[2]]
}
.set { ch_for_mix }

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