Merge pull request #1563 from YeHW/vep_species_suffix

Fix: Correct vep_cache_path_full when refseq/merged option is present

CHANGELOG.md

@@ -32,6 +32,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#1542](https://github.com/nf-core/sarek/pull/1542) - Removing legacy configs of `CUSTOM_DUMPSOFTWAREVERSIONS`
 - [#1547](https://github.com/nf-core/sarek/pull/1547) - Correct typo in help text in nextflow_schema.json
 - [#1556](https://github.com/nf-core/sarek/pull/1556) - Fix display of some commands in `docs/usage.md`
+- [#1563](https://github.com/nf-core/sarek/pull/1563) - Fix `vep_cache_path_full` so that `--refseq/--merged` will work for ENSEMBLVEP
 
 ### Removed
 

README.md

@@ -149,6 +149,7 @@ We thank the following people for their extensive assistance in the development
 - [Grant Neilson](https://github.com/grantn5)
 - [gulfshores](https://github.com/gulfshores)
 - [Harshil Patel](https://github.com/drpatelh)
+- [Hongwei Ye](https://github.com/YeHW)
 - [James A. Fellows Yates](https://github.com/jfy133)
 - [Jesper Eisfeldt](https://github.com/J35P312)
 - [Johannes Alneberg](https://github.com/alneberg)

main.nf

@@ -253,6 +253,7 @@ workflow NFCORE_SAREK {
             params.vep_species,
             params.vep_cache_version,
             params.vep_genome,
+            params.vep_custom_args,
             "Please refer to https://nf-co.re/sarek/docs/usage/#how-to-customise-snpeff-and-vep-annotation for more information.")
 
             snpeff_cache = ANNOTATION_CACHE_INITIALISATION.out.snpeff_cache

subworkflows/local/annotation_cache_initialisation/main.nf

@@ -19,6 +19,7 @@ workflow ANNOTATION_CACHE_INITIALISATION {
     vep_species
     vep_cache_version
     vep_genome
+    vep_custom_args
     help_message
 
     main:
@@ -39,7 +40,8 @@ workflow ANNOTATION_CACHE_INITIALISATION {
 
     if (vep_enabled) {
         def vep_annotation_cache_key = (vep_cache == "s3://annotation-cache/vep_cache/") ? "${vep_cache_version}_${vep_genome}/" : ""
-        def vep_cache_dir = "${vep_annotation_cache_key}${vep_species}/${vep_cache_version}_${vep_genome}"
+        def vep_species_suffix = vep_custom_args.contains("--merged") ? '_merged' : (vep_custom_args.contains("--refseq") ? '_refseq' : '')
+        def vep_cache_dir = "${vep_annotation_cache_key}${vep_species}${vep_species_suffix}/${vep_cache_version}_${vep_genome}"
         def vep_cache_path_full = file("$vep_cache/$vep_cache_dir", type: 'dir')
         if ( !vep_cache_path_full.exists() || !vep_cache_path_full.isDirectory() ) {
             if (vep_cache == "s3://annotation-cache/vep_cache/") {