Change to value channel

nf-core · Aug 16, 2024 · 1542401 · 1542401
1 parent 514c81a
commit 1542401
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/main.nf b/main.nf
@@ -177,7 +177,7 @@ workflow NFCORE_SAREK {
     rt_file                = PREPARE_GENOME.out.rt_file
 
     // Tabix indexed vcf files
-    bcftools_annotations_tbi  = params.bcftools_annotations    ? params.bcftools_annotations_tbi ? Channel.fromPath(params.bcftools_annotations_tbi).collect() : PREPARE_GENOME.out.bcftools_annotations_tbi : Channel.empty()
+    bcftools_annotations_tbi  = params.bcftools_annotations    ? params.bcftools_annotations_tbi ? Channel.fromPath(params.bcftools_annotations_tbi).collect() : PREPARE_GENOME.out.bcftools_annotations_tbi : Channel.value([])
     dbsnp_tbi                 = params.dbsnp                   ? params.dbsnp_tbi                ? Channel.fromPath(params.dbsnp_tbi).collect()                : PREPARE_GENOME.out.dbsnp_tbi                : Channel.value([])
     germline_resource_tbi     = params.germline_resource       ? params.germline_resource_tbi    ? Channel.fromPath(params.germline_resource_tbi).collect()    : PREPARE_GENOME.out.germline_resource_tbi    : [] //do not change to Channel.value([]), the check for its existence then fails for Getpileupsumamries
     known_indels_tbi          = params.known_indels            ? params.known_indels_tbi         ? Channel.fromPath(params.known_indels_tbi).collect()         : PREPARE_GENOME.out.known_indels_tbi         : Channel.value([])