Merge pull request #688 from BarryDigby/vep_plugins

Vep plugins
nf-core · Jul 26, 2022 · 5267449 · 5267449
2 parents 648a24d + cb423cf
commit 5267449
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -1211,9 +1211,9 @@ process{
             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,'${params.dbnsfp_consequence}',${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=${params.spliceai_snv.split("/")[-1]},${params.spliceai_indel.split("/")[-1]}"                  : '',
+                (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()