Merge pull request #1196 from maxulysse/annotation_cache_keys

More sensible default for use_annotation_cache_keys

Author: maxulysse

CHANGELOG.md

@@ -16,7 +16,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#1158](https://github.com/nf-core/sarek/pull/1158) - Add preprint
 - [#1159](https://github.com/nf-core/sarek/pull/1159) - ISMB Poster
 - [#1173](https://github.com/nf-core/sarek/pull/1173) - CI tests for VQSR track with stub runs
-- [#1122](https://github.com/nf-core/sarek/pull/1122) - Add `annotation cache` functionality
+- [#1122](https://github.com/nf-core/sarek/pull/1122), [#1196](https://github.com/nf-core/sarek/pull/1196) - Add `annotation cache` functionality
 - [#1184](https://github.com/nf-core/sarek/pull/1184) - Stub-based CI-test of Sentieon joint-germline variant-calling with VQSR
 
 ### Changed

conf/test_full.config

@@ -19,7 +19,8 @@ params {
 
     // Other params
     tools = 'strelka,mutect2,freebayes,ascat,manta,cnvkit,tiddit,controlfreec,vep'
-    split_fastq            = 20000000
-    intervals              = 's3://ngi-igenomes/test-data/sarek/S07604624_Padded_Agilent_SureSelectXT_allexons_V6_UTR.bed'
-    wes                    = true
+    split_fastq               = 20000000
+    intervals                 = 's3://ngi-igenomes/test-data/sarek/S07604624_Padded_Agilent_SureSelectXT_allexons_V6_UTR.bed'
+    wes                       = true
+    use_annotation_cache_keys = true
 }

conf/test_full_germline.config

@@ -19,6 +19,6 @@ params {
 
     // Other params
     tools = 'strelka,freebayes,haplotypecaller,deepvariant,manta,tiddit,cnvkit,vep'
-
-    split_fastq = 50000000
+    split_fastq               = 50000000
+    use_annotation_cache_keys = true
 }

nextflow.config

@@ -83,7 +83,7 @@ params {
     spliceai_indel_tbi        = null // No spliceai_indel file index
     spliceai_snv              = null // No spliceai_snv file
     spliceai_snv_tbi          = null // No spliceai_snv file index
-    use_annotation_cache_keys = true
+    use_annotation_cache_keys = false
     vep_cache                 = 's3://annotation-cache/vep_cache/'
     vep_custom_args           = "--everything --filter_common --per_gene --total_length --offline --format vcf" // Default arguments for VEP
     vep_dbnsfp                = null // dbnsfp plugin disabled within VEP