Merge pull request #1628 from cmatKhan/fix_dbsnp_if_null

Allow dbsnp if null in germline variant calling
nf-core · Aug 23, 2024 · 7871b03 · 7871b03
2 parents 8fcc094 + e0cbf05
commit 7871b03
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -18,6 +18,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Fixed
 
 - [1623](https://github.com/nf-core/sarek/pull/1623) - Update docs to clarify vep cache folder organisation
+- [1628](https://github.com/nf-core/sarek/pull/1628) - Fix dbsnp channel mapping in germline variant calling subworkflow
 
 ### Removed
 

diff --git a/subworkflows/local/bam_variant_calling_germline_all/main.nf b/subworkflows/local/bam_variant_calling_germline_all/main.nf
@@ -130,8 +130,8 @@ workflow BAM_VARIANT_CALLING_GERMLINE_ALL {
             fasta,
             fasta_fai,
             dict,
-            dbsnp.map{ it -> [[id:it[0].baseName], it] },
-            dbsnp_tbi.map{ it -> [[id:it[0].baseName], it] },
+            dbsnp.map{it -> [[:], it]},
+            dbsnp_tbi.map{it -> [[:], it]},
             intervals)
 
         vcf_haplotypecaller = BAM_VARIANT_CALLING_HAPLOTYPECALLER.out.vcf