Merge pull request nf-core#106 from nf-core/bounlu-patch-2

maxulysse · web-flow · commit 0429e5799e69 · 2024-02-12T11:19:44.000+01:00
fix vep_cache
diff --git a/workflows/rnavar.nf b/workflows/rnavar.nf
@@ -156,7 +156,7 @@ if (params.vep_cache && params.annotate_tools && (params.annotate_tools.split(',
     } else {
         vep_annotation_cache_key = params.use_annotation_cache_keys ? "${params.vep_cache_version}_${params.vep_genome}/" : ""
     }
-    def vep_cache_dir = "${vep_annotation_cache_key}${params.vep_species}/${params.vep_cache_version}_${params.vep_genome}"
+    def vep_cache_dir = "${vep_annotation_cache_key}${params.vep_cache_version}_${params.vep_genome}/${params.vep_species}"
     def vep_cache_path_full = file("$params.vep_cache/$vep_cache_dir", type: 'dir')
     if ( !vep_cache_path_full.exists() || !vep_cache_path_full.isDirectory() ) {
         if (params.vep_cache == "s3://annotation-cache/vep_cache") {

Original file line number	Diff line number	Diff line change
`@@ -156,7 +156,7 @@ if (params.vep_cache && params.annotate_tools && (params.annotate_tools.split(',`
`156`	`156`	`} else {`
`157`	`157`	`vep_annotation_cache_key = params.use_annotation_cache_keys ? "${params.vep_cache_version}_${params.vep_genome}/" : ""`
`158`	`158`	`}`
`159`		`- def vep_cache_dir = "${vep_annotation_cache_key}${params.vep_species}/${params.vep_cache_version}_${params.vep_genome}"`
	`159`	`+ def vep_cache_dir = "${vep_annotation_cache_key}${params.vep_cache_version}_${params.vep_genome}/${params.vep_species}"`
`160`	`160`	`def vep_cache_path_full = file("$params.vep_cache/$vep_cache_dir", type: 'dir')`
`161`	`161`	`if ( !vep_cache_path_full.exists() \|\| !vep_cache_path_full.isDirectory() ) {`
`162`	`162`	`if (params.vep_cache == "s3://annotation-cache/vep_cache") {`