diff --git a/snappy_pipeline/workflows/somatic_variant_filtration/__init__.py b/snappy_pipeline/workflows/somatic_variant_filtration/__init__.py index 2581b639c..f56353c6a 100644 --- a/snappy_pipeline/workflows/somatic_variant_filtration/__init__.py +++ b/snappy_pipeline/workflows/somatic_variant_filtration/__init__.py @@ -410,6 +410,7 @@ def input_function(wildcards): filter_nb = int(wildcards["filter_nb"]) ebfilter_config = self.config["filter_list"][filter_nb - 1][self.filter_name] parameters.update(ebfilter_config) + parameters["has_annotation"] = self.config.get("has_annotation", False) return parameters return input_function @@ -731,6 +732,7 @@ def get_params(self, action): self._validate_action(action) parameters = self.config["eb_filter"] parameters.update(self.config["filter_sets"]["dkfz_and_ebfilter"]) + parameters["has_annotation"] = self.config.get("has_annotation", False) return parameters @dictify diff --git a/snappy_wrappers/wrappers/eb_filter/wrapper.py b/snappy_wrappers/wrappers/eb_filter/wrapper.py index 2e5f4b28e..e35444e8e 100644 --- a/snappy_wrappers/wrappers/eb_filter/wrapper.py +++ b/snappy_wrappers/wrappers/eb_filter/wrapper.py @@ -8,6 +8,7 @@ params = dict(snakemake.params)["args"] filter_name = params["filter_name"] if "filter_name" in params else "" +has_annotation = str(params["has_annotation"] if "has_annotation" in params else False) if "interval" in params: cmd_fetch = "tabix --print-header {} {}".format( @@ -61,7 +62,11 @@ filter=$(echo "$filter" | sed -e "s/^ || //") ann="CSQ" zgrep -q "^##INFO=