Merge pull request #1089 from maxulysse/duplication

FIX: Remove duplicated code
nf-core · Jun 9, 2023 · bce4a4c · bce4a4c
2 parents 5c2017d + 7fcf0fc
commit bce4a4c
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -15,6 +15,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Fixed
 
 - [#1087](https://github.com/nf-core/sarek/pull/1087) - Fix wrong default memory in GATK4_CREATESEQUENCEDICTIONARY [#1085](https://github.com/nf-core/sarek/pull/1085)
+- [#1089](https://github.com/nf-core/sarek/pull/1089) - Remove duplicated code
 
 ## [3.2.1](https://github.com/nf-core/sarek/releases/tag/3.2.1) - Pierikjaure
 

diff --git a/workflows/sarek.nf b/workflows/sarek.nf
@@ -147,7 +147,6 @@ fasta_fai          = params.fasta_fai          ? Channel.fromPath(params.fasta_f
 germline_resource  = params.germline_resource  ? Channel.fromPath(params.germline_resource).collect() : Channel.value([]) // Mutec2 does not require a germline resource, so set to optional input
 known_indels       = params.known_indels       ? Channel.fromPath(params.known_indels).collect()      : Channel.value([])
 known_snps         = params.known_snps         ? Channel.fromPath(params.known_snps).collect()        : Channel.value([])
-known_snps         = params.known_snps         ? Channel.fromPath(params.known_snps).collect()        : Channel.value([])
 mappability        = params.mappability        ? Channel.fromPath(params.mappability).collect()       : Channel.value([])
 pon                = params.pon                ? Channel.fromPath(params.pon).collect()               : Channel.value([]) // PON is optional for Mutect2 (but highly recommended)