variant-annotator: get genome release from config for use in wrapper.

bihealth · May 2, 2022 · 9a5b739 · 9a5b739
1 parent d50b85d
commit 9a5b739
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Showing 2 changed files with 2 additions and 2 deletions.
diff --git 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
@@ -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]} \