fix: eb_filter wrapper assuming ANN/CSQ is present

snappy_pipeline/workflows/somatic_variant_filtration/__init__.py

@@ -502,11 +502,13 @@ def get_input_files(self, action):
         """Return path to jannovar-annotated vcf input file"""
         # Validate action
         self._validate_action(action)
+
+        name_pattern = "{mapper}.{var_caller}"
+        if self.config["has_annotation"]:
+            name_pattern += ".{annotator}"
+
         # VCF file and index
-        tpl = (
-            "output/{mapper}.{var_caller}.{annotator}.{tumor_library}/out/"
-            "{mapper}.{var_caller}.{annotator}.{tumor_library}"
-        )
+        tpl = f"output/{name_pattern}." "{tumor_library}/" f"out/{name_pattern}." "{tumor_library}"
         key_ext = {"vcf": ".vcf.gz", "vcf_tbi": ".vcf.gz.tbi"}
         somatic_variant = self.parent.sub_workflows["somatic_variant"]
         for key, ext in key_ext.items():
@@ -523,10 +525,16 @@ def get_output_files(self, action):
         """Return output files for the filtration"""
         # Validate action
         self._validate_action(action)
+
+        name_pattern = "{mapper}.{var_caller}"
+        if self.config["has_annotation"]:
+            name_pattern += ".{annotator}"
+
         prefix = (
-            r"work/{mapper}.{var_caller}.{annotator}."
-            r"dkfz_bias_filter.{tumor_library,[^\.]+}/out/{mapper}.{var_caller}."
-            r"{annotator}.dkfz_bias_filter.{tumor_library}"
+            rf"work/{name_pattern}."
+            r"dkfz_bias_filter.{tumor_library,[^\.]+}/"
+            rf"out/{name_pattern}."
+            r"dkfz_bias_filter.{tumor_library}"
         )
         key_ext = {
             "vcf": ".vcf.gz",
@@ -588,11 +596,15 @@ def get_input_files(self, action):
 
     @dictify
     def _get_input_files_run(self, wildcards):
+        name_pattern = "{mapper}.{var_caller}"
+        if self.config["has_annotation"]:
+            name_pattern += ".{annotator}"
         # VCF file and index
         tpl = (
-            "work/{mapper}.{var_caller}.{annotator}."
-            "dkfz_bias_filter.{tumor_library}/out/{mapper}.{var_caller}."
-            "{annotator}.dkfz_bias_filter."
+            f"work/{name_pattern}."
+            "dkfz_bias_filter.{tumor_library}/"
+            f"out/{name_pattern}."
+            "dkfz_bias_filter."
             "{tumor_library}"
         )
         key_ext = {"vcf": ".vcf.gz", "vcf_tbi": ".vcf.gz.tbi"}
@@ -619,10 +631,14 @@ def get_output_files(self, action):
 
     @dictify
     def _get_output_files_run(self):
+        name_pattern = "{mapper}.{var_caller}"
+        if self.config["has_annotation"]:
+            name_pattern += ".{annotator}"
+        # VCF file and index
         prefix = (
-            r"work/{mapper}.{var_caller}.{annotator}."
-            r"dkfz_bias_filter.eb_filter.{tumor_library,[^\.]+}/out/"
-            r"{mapper}.{var_caller}.{annotator}."
+            rf"work/{name_pattern}."
+            r"dkfz_bias_filter.eb_filter.{tumor_library,[^\.]+}/"
+            rf"out/{name_pattern}."
             r"dkfz_bias_filter.eb_filter.{tumor_library}"
         )
         key_ext = {

snappy_wrappers/wrappers/eb_filter/wrapper.py

@@ -15,6 +15,7 @@
 
 step = snakemake.config["pipeline_step"]["name"]
 config = snakemake.config["step_config"][step]
+has_annotation = str(config.get("has_annotation", False))
 
 if "ebfilter_threshold" in config:
     threshold = config.get("ebfilter_threshold", 0)
@@ -86,7 +87,11 @@
     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" \