removed redundant vep_repo_path from config

pipelines/annotations.snakefile

@@ -38,8 +38,7 @@ bcf_dir = Path(config["bcf_dir"])
 anno_tmp_dir = Path(config["anno_tmp_dir"])
 anno_dir = Path(config["anno_dir"])
 metadata_dir = Path(config["metadata_dir"])
-vep_plugin_repo = Path(config["vep_plugin_repo"])
-condel_config_path = vep_plugin_repo / "config" / "Condel" / "config"
+condel_config_path = vep_plugin_dir / "config" / "Condel" / "config"
 
 
 # init cadd PLugin

pipelines/config/deeprvat_annotation_config.yaml

@@ -15,7 +15,7 @@ anno_tmp_dir : output_dir/annotations/tmp
 anno_dir : output_dir/annotations
 
 vep_cache_dir : repo_dir/ensembl-vep/cache/vep109
-vep_plugin_dir : repo_dir/ensembl-vep/Plugins
+vep_plugin_dir : repo_dir/VEP_Plugins
 spliceAI_snv_file : annotation_data/spliceAI/spliceai_scores.raw.snv.hg38.vcf.gz
 spliceAI_indel_file : annotation_data/spliceAI/spliceai_scores.raw.indel.hg38.vcf.gz
 primateAI_file : annotation_data/primateAI/PrimateAI_scores_v0.2_GRCh38_sorted.tsv.bgz
@@ -26,7 +26,6 @@ deeprvat_repo_dir : deeprvat_repo_dir
 kipoiveff_repo_dir : repo_dir/kipoi-veff2
 faatpipe_repo_dir : repo_dir/faatpipe
 vep_repo_dir : repo_dir/ensembl-vep
-vep_plugin_repo : repo_dir/VEP_plugins
 variant_file_path : preprocessing_workdir/norm/variants/variants.tsv.gz
 pybedtools_tmp_path : output_dir/annotations/tmp/pybedtools
 n_jobs_deepripe : 32