Merge pull request #706 from FriederikeHanssen/loftee

Vep Issues: loftee needs version
nf-core · Aug 16, 2022 · cdf68a8 · cdf68a8
2 parents 1a7a571 + eb4bc9c
commit cdf68a8
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -24,6 +24,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#688](https://github.com/nf-core/sarek/pull/688) - Fixed VEP plugins issue cf [#687](https://github.com/nf-core/sarek/issues/687)
 - [#689](https://github.com/nf-core/sarek/pull/689) - Fixed when clause for non `BWA mem` building mapping indexes
 - [#704](https://github.com/nf-core/sarek/pull/704) - Fixed `cf_ploidy` to string instead of number
+- [#706](https://github.com/nf-core/sarek/pull/706) - Fixed `vep_version` not found error when running `--vep_loftee`
 
 ### Deprecated
 

diff --git a/conf/modules.config b/conf/modules.config
@@ -1208,15 +1208,15 @@ process{
     // VEP
     if (params.tools && (params.tools.split(',').contains('vep') || params.tools.split(',').contains('merge'))) {
         withName: 'ENSEMBLVEP' {
-            ext.args          = [
+            ext.args          = { [
                 '--everything --filter_common --per_gene --total_length --offline --format vcf',
                 (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-${params.vep_version}-0" : '',
                 (params.vep_spliceai && params.spliceai_snv && params.spliceai_indel) ? "--plugin SpliceAI,snv=${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'
-            ].join(' ').trim()
+            ].join(' ').trim() }
             // If just VEP: <vcf prefix>_VEP.ann.vcf
             ext.prefix       = { "${vcf.baseName.minus(".vcf")}_VEP" }
             if (!params.vep_cache)    container = { params.vep_genome ? "nfcore/vep:${params.vep_version}.${params.vep_genome}" : "nfcore/vep:${params.vep_version}.${params.genome}" }