moved the function to the process itself

nf-cmgg · Oct 24, 2023 · e5eeff6 · e5eeff6
1 parent 3b05385
commit e5eeff6
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Showing 7 changed files with 45 additions and 13 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -32,7 +32,6 @@ process {
 
     if(params.annotate) {
         withName: '^.*:ENSEMBLVEP_DOWNLOAD\$' {
-            container = {DynamicContainers.findLatest("ensembl-vep", params.vep_version, workflow.containerEngine)}
             ext.args = "--AUTO c --CONVERT --NO_BIOPERL --NO_TEST --NO_UPDATE"
         }
     }
@@ -263,7 +262,6 @@ process {
             }
 
             withName: "^.*VCF_ANNOTATE_VEP_ANNOTSV_VCFANNO:ENSEMBLVEP_VEP\$" {
-                container = {DynamicContainers.findLatest("ensembl-vep", params.vep_version, workflow.containerEngine)}
                 ext.prefix = {"${meta.id}_annotated"}
                 ext.args = {[
                     // specify we use VCF files

diff --git a/modules.json b/modules.json
@@ -50,12 +50,14 @@
                     "ensemblvep/download": {
                         "branch": "master",
                         "git_sha": "9f9e1fc31cb35876922070c0e601ae05abae5cae",
-                        "installed_by": ["modules"]
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/ensemblvep/download/ensemblvep-download.diff"
                     },
                     "ensemblvep/vep": {
                         "branch": "master",
                         "git_sha": "9f9e1fc31cb35876922070c0e601ae05abae5cae",
-                        "installed_by": ["modules"]
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/ensemblvep/vep/ensemblvep-vep.diff"
                     },
                     "expansionhunter": {
                         "branch": "master",

diff --git a/modules/nf-core/ensemblvep/download/ensemblvep-download.diff b/modules/nf-core/ensemblvep/download/ensemblvep-download.diff
diff --git a/modules/nf-core/ensemblvep/download/main.nf b/modules/nf-core/ensemblvep/download/main.nf
diff --git a/modules/nf-core/ensemblvep/vep/ensemblvep-vep.diff b/modules/nf-core/ensemblvep/vep/ensemblvep-vep.diff
diff --git a/modules/nf-core/ensemblvep/vep/main.nf b/modules/nf-core/ensemblvep/vep/main.nf
diff --git a/nextflow.config b/nextflow.config
@@ -39,7 +39,7 @@ params {
     // VEP options
     vep_assembly                    = "GRCh38"
     vep_cache_version               = 108
-    vep_version                     = 108.2
+    vep_version                     = 109.3
     species                         = "homo_sapiens"
     vep_phenotypes                  = false