Merge pull request #587 from maxulysse/dev_vep_mix_fix

fix: VEP - Unknown method invocation on ArrayList type

Author: maxulysse

CHANGELOG.md

@@ -84,7 +84,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#524](https://github.com/nf-core/sarek/pull/524) - Fix intervals usage by counting the actual list of scatter/gather files produced and not overall number of intervals
 - [#549](https://github.com/nf-core/sarek/pull/549) - Fix unique lanes required for Freebayes: issue [#311](https://github.com/nf-core/sarek/issues/311), replaces `meta.clone()` with actual copy of map to avoid issues with <https://nfcore.slack.com/archives/C027CM7P08M/p1644241819942339>
 - [#567](https://github.com/nf-core/sarek/pull/567) - Fix interval name resolving during scatter/gather by moving logic to modules.config causing name to be correctly resolved on process execution; also fixed duplicate naming when variant callers produce multiple vcf files by adding field `type` to `meta` map
-- [#585](https://github.com/nf-core/sarek/pull/585) - Fix Spark usage for GATK4 modules.
+- [#585](https://github.com/nf-core/sarek/pull/585) - Fix Spark usage for GATK4 modules
+- [#587](https://github.com/nf-core/sarek/pull/587) - Fix issue with VEP extra files
 
 ### Deprecated
 

workflows/sarek.nf

@@ -103,19 +103,15 @@ vep_cache          = params.vep_cache          ? Channel.fromPath(params.vep_cac
 vep_extra_files = []
 
 if (params.dbnsfp && params.dbnsfp_tbi) {
-    vep_extra_files = vep_extra_files.mix(
-        Channel.fromPath(params.dbnsfp),
-        Channel.fromPath(params.dbnsfp_tbi)
-    ).collect()
+    vep_extra_files.add(file(params.dbnsfp, checkIfExists: true))
+    vep_extra_files.add(file(params.dbnsfp_tbi, checkIfExists: true))
 }
 
 if (params.spliceai_snv && params.spliceai_snv_tbi && params.spliceai_indel && params.spliceai_indel_tbi) {
-    vep_extra_files = vep_extra_files.mix(
-        Channel.fromPath(params.spliceai_indel),
-        Channel.fromPath(params.spliceai_indel_tbi),
-        Channel.fromPath(params.spliceai_snv),
-        Channel.fromPath(params.spliceai_snv_tbi)
-    ).collect()
+    vep_extra_files.add(file(params.spliceai_indel, checkIfExists: true))
+    vep_extra_files.add(file(params.spliceai_indel_tbi, checkIfExists: true))
+    vep_extra_files.add(file(params.spliceai_snv, checkIfExists: true))
+    vep_extra_files.add(file(params.spliceai_snv_tbi, checkIfExists: true))
 }
 
 // Initialize value channels based on params, not defined within the params.genomes[params.genome] scope