Added VCF to output.

snappy_pipeline/workflows/repeat_expansion/__init__.py

@@ -12,10 +12,11 @@
     AnnotateExpansionHunter,
 )
 
-#: Extensions of files to create as main payload
-EXT_VALUES = (".json", ".json.md5")
-
-#: Default configuration for the repeat_expansion step
+#: Extensions of files to create as main payload - JSON.
+EXT_JSON = (".json", ".json.md5")
+#: Extensions of files to create as main payload - VCF.
+EXT_VCF = (".vcf", ".vcf.md5")
+#: Default configuration for the repeat_expansion step.
 DEFAULT_CONFIG = r"""
 # Default configuration repeat_expansion
 step_config:
@@ -124,11 +125,14 @@ def _get_input_files_annotate(_wildcards):
     @dictify
     def _get_output_files_run():
         """Yield output files' patterns for rule `run` - ExpansionHunter call."""
-        ext = "json"
+        # Initialise variables
         name_pattern = "{mapper}.expansionhunter.{library_name}"
-        yield ext, "work/{name_pattern}/out/{name_pattern}.{ext}".format(
-            name_pattern=name_pattern, ext=ext
-        )
+        ext_dict = {"json": "json", "vcf": "vcf", "vcf_md5": "vcf.md5"}
+        # Yield
+        for key, ext in ext_dict.items():
+            yield key, "work/{name_pattern}/out/{name_pattern}.{ext}".format(
+                name_pattern=name_pattern, ext=ext
+            )
 
     @staticmethod
     @dictify
@@ -218,14 +222,23 @@ def _all_donors(self, include_background=True):
     @listify
     def get_result_files(self):
         """Return list of result files for the germline repeat expansion analysis workflow."""
-        # Actually yield the result files.
-        name_pattern = "{mapper}.{tool}_annotated.{donor.dna_ngs_library.name}"
+        # Initialise variable
         tools = ("expansionhunter",)
+        # Yield the JSON annotated results files
+        name_pattern = "{mapper}.{tool}_annotated.{donor.dna_ngs_library.name}"
+        yield from self._yield_result_files(
+            os.path.join("output", name_pattern, "out", name_pattern + "{ext}"),
+            mapper=self.w_config["step_config"]["ngs_mapping"]["tools"]["dna"],
+            tool=tools,
+            ext=EXT_JSON,
+        )
+        # Yield the VCF results files
+        name_pattern = "{mapper}.{tool}.{donor.dna_ngs_library.name}"
         yield from self._yield_result_files(
             os.path.join("output", name_pattern, "out", name_pattern + "{ext}"),
             mapper=self.w_config["step_config"]["ngs_mapping"]["tools"]["dna"],
             tool=tools,
-            ext=EXT_VALUES,
+            ext=EXT_VCF,
         )
 
     def _yield_result_files(self, tpl, **kwargs):

snappy_wrappers/wrappers/expansionhunter/wrapper.py

@@ -47,9 +47,10 @@
 """
 )
 
-# Compute MD5 sums of logs.
+# Compute MD5 sums of log and vcf.
 shell(
     r"""
 md5sum {snakemake.log} >{snakemake.log}.md5
+md5sum {snakemake.output.vcf} >{snakemake.output.vcf_md5}
 """
 )

tests/snappy_pipeline/workflows/test_workflows_repeat_expansion.py

@@ -77,18 +77,30 @@ def test_repeat_expansion_workflow_files(repeat_expansion_workflow):
     to the expected results for ExpansionHunter.
     """
     # Define expected
-    pattern_out = (
+    pattern_json_out = (
         "output/bwa.expansionhunter_annotated.P00{i}-N1-DNA1-WGS1/out/"
         "bwa.expansionhunter_annotated.P00{i}-N1-DNA1-WGS1.{ext}"
     )
+    pattern_vcf_out = (
+        "output/bwa.expansionhunter.P00{i}-N1-DNA1-WGS1/out/"
+        "bwa.expansionhunter.P00{i}-N1-DNA1-WGS1.{ext}"
+    )
     expected = [
-        pattern_out.format(i=i, ext=ext)
+        pattern_json_out.format(i=i, ext=ext)
         for i in range(1, 7)  # all donors: P001 - P006
         for ext in (
             "json",
             "json.md5",
         )
     ]
+    expected += [
+        pattern_vcf_out.format(i=i, ext=ext)
+        for i in range(1, 7)  # all donors: P001 - P006
+        for ext in (
+            "vcf",
+            "vcf.md5",
+        )
+    ]
     # Get actual
     actual = repeat_expansion_workflow.get_result_files()
     assert sorted(actual) == sorted(expected)
@@ -110,13 +122,18 @@ def test_expansionhunter_run_step_part_get_input_files(repeat_expansion_workflow
 def test_expansionhunter_run_step_part_get_output_files(repeat_expansion_workflow):
     """Tests ExpansionHunterStepPart::_get_output_files_run()"""
     # Define expected
-    json_out = (
+    pattern_out = (
         "work/{mapper}.expansionhunter.{library_name}/out/"
-        "{mapper}.expansionhunter.{library_name}.json"
+        "{mapper}.expansionhunter.{library_name}"
     )
-    expected = {"json": json_out}
+    expected = {
+        "json": pattern_out + ".json",
+        "vcf": pattern_out + ".vcf",
+        "vcf_md5": pattern_out + ".vcf.md5",
+    }
     # Get actual
     actual = repeat_expansion_workflow.get_output_files("expansionhunter", "run")
+    print(actual)
     assert actual == expected