Merge branch 'dev' into annotation_cache

nf-core · Nov 1, 2023 · 290f018 · 290f018
2 parents 24d7666 + e72d4e4
commit 290f018
Show file tree

Hide file tree

Showing 4 changed files with 10 additions and 1 deletion.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -18,6 +18,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - [#1278](https://github.com/nf-core/sarek/pull/1278) - Hide sentieon parameters similar to other variant callers
 - [#1280](https://github.com/nf-core/sarek/pull/1280) - Replacing link to `SentieonDNAscopeModel1.1.model` in Sentieon's S3 with link to same file in igenomes' S3
+- [#1303](https://github.com/nf-core/sarek/pull/1303) - Ressurect vep_version params and changed its scope to pipeline to enable usage for vep loftee plugin
 
 ### Fixed
 

diff --git a/conf/modules/annotate.config b/conf/modules/annotate.config
@@ -37,7 +37,7 @@ process {
             ext.args         = { [
                 (params.vep_dbnsfp && params.dbnsfp && !params.dbnsfp_consequence)    ? "--plugin dbNSFP,${params.dbnsfp.split("/")[-1]},${params.dbnsfp_fields}"                                              : '',
                 (params.vep_dbnsfp && params.dbnsfp && params.dbnsfp_consequence)     ? "--plugin dbNSFP,'consequence=${params.dbnsfp_consequence}',${params.dbnsfp.split("/")[-1]},${params.dbnsfp_fields}"   : '',
-                (params.vep_loftee)                                                   ? "--plugin LoF,loftee_path:/opt/conda/envs/nf-core-vep-${params.vep_version}/share/ensembl-vep-${params.vep_version}-0" : '',
+                (params.vep_loftee)                                                   ? "--plugin LoF,loftee_path://usr/local/share/ensembl-vep-${params.vep_version}" : '',
                 (params.vep_spliceai && params.spliceai_snv && params.spliceai_indel) ? "--plugin SpliceAI,snv=${params.spliceai_snv.split("/")[-1]},indel=${params.spliceai_indel.split("/")[-1]}"            : '',
                 (params.vep_spliceregion)                                             ? '--plugin SpliceRegion'                                                                                                : '',
                 (params.vep_out_format)                                               ? "--${params.vep_out_format}"                                                                                           : '--vcf',

diff --git a/nextflow.config b/nextflow.config
@@ -94,6 +94,7 @@ params {
     vep_out_format            = "vcf"
     vep_spliceai              = null // spliceai plugin disabled within VEP
     vep_spliceregion          = null // spliceregion plugin disabled within VEP
+    vep_version               = "110.0-0"      // Should be updated when we update VEP, needs this to get full path to some plugins
     bcftools_annotations               = null  // No extra annotation file
     bcftools_annotations_index         = null  // No extra annotation file index
     bcftools_header_lines              = null  // No header lines to be added to the VCF file

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -540,6 +540,13 @@
                     "description": "Add an extra custom argument to VEP.",
                     "help_text": "Using this params you can add custom args to VEP."
                 },
+                "vep_version": {
+                    "type": "string",
+                    "default": "110.0-0",
+                    "fa_icon": "fas fa-toolbox",
+                    "description": "Should reflect the VEP version used in the container.",
+                    "help_text": "Used by the loftee plugin that need the full path."
+                },
                 "outdir_cache": {
                     "type": "string",
                     "format": "directory-path",