fix: eb_filter wrapper assuming ANN/CSQ is present (#506)

bihealth · May 6, 2024 · 4dc4948 · 4dc4948
1 parent 66f555c
commit 4dc4948
Show file tree

Hide file tree

Showing 3 changed files with 9 additions and 2 deletions.
diff --git 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
@@ -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=<ID=CSQ," {snakemake.input.vcf} || ann="ANN"
-    filter="$filter || $ann ~ \"stream_gene_variant\""
+    if [[ '{has_annotation}' == "True" ]]; then
+        filter="$filter || $ann ~ \"stream_gene_variant\""
+    else
+        filter="$filter"
+    fi
     {cmd_fetch} \
     | bcftools view \
         -e "$filter" \

diff --git a/tests/snappy_pipeline/workflows/test_workflows_somatic_variant_filtration.py b/tests/snappy_pipeline/workflows/test_workflows_somatic_variant_filtration.py
@@ -562,7 +562,7 @@ def test_one_filter_step_part_get_params(somatic_variant_filtration_workflow_lis
     assert actual == expected
 
     wildcards = Wildcards(fromdict={"filter_nb": 2})
-    expected = {"filter_name": "ebfilter_2", "threshold": 2.3}
+    expected = {"filter_name": "ebfilter_2", "threshold": 2.3, "has_annotation": True}
     actual = somatic_variant_filtration_workflow_list.get_params("one_ebfilter", "run")(wildcards)
     assert actual == expected