this adjusts the dbsnp channel mapping in variant_calling_germline_al…

…l to match variant_calling_sentieon_dnascope. null values are handled appropriately this way
famosab · Aug 21, 2024 · c9a55b8 · c9a55b8
1 parent c592225
commit c9a55b8
Showing 1 changed file with 2 additions and 2 deletions.
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