diff --git a/snappy_pipeline/workflows/variant_export/__init__.py b/snappy_pipeline/workflows/variant_export/__init__.py index 66666cbda..8f389b8c9 100644 --- a/snappy_pipeline/workflows/variant_export/__init__.py +++ b/snappy_pipeline/workflows/variant_export/__init__.py @@ -82,6 +82,7 @@ path_variant_calling: ../variant_calling tools_ngs_mapping: null tools_variant_calling: null + release: GRCh37 # REQUIRED: default 'GRCh37' path_exon_bed: REQUIRED # REQUIRED: exon BED file to use when handling WGS data path_refseq_ser: REQUIRED # REQUIRED: path to RefSeq .ser file path_ensembl_ser: REQUIRED # REQUIRED: path to ENSEMBL .ser file diff --git a/snappy_wrappers/wrappers/varfish_annotator/annotate/wrapper.py b/snappy_wrappers/wrappers/varfish_annotator/annotate/wrapper.py index 2eaf2b961..6e416176b 100644 --- a/snappy_wrappers/wrappers/varfish_annotator/annotate/wrapper.py +++ b/snappy_wrappers/wrappers/varfish_annotator/annotate/wrapper.py @@ -16,7 +16,6 @@ annotation_args = [] # TODO: care about case of WGS data -# TODO: properly handle release # TODO: remove case ID parameter from annotator shell( @@ -81,7 +80,7 @@ -XX:MaxHeapSize=10g \ -XX:+UseConcMarkSweepGC \ \ - --release GRCh37 \ + --release {export_config[release]} \ \ --ref-path {snakemake.config[static_data_config][reference][path]} \ --db-path {export_config[path_db]} \