wip

snappy_pipeline/workflows/common/delly.py

@@ -18,10 +18,10 @@
 
 
 class Delly2StepPart(
-    ForwardSnakemakeFilesMixin,
-    ForwardResourceUsageMixin,
     SvCallingGetResultFilesMixin,
     SvCallingGetLogFileMixin,
+    ForwardSnakemakeFilesMixin,
+    ForwardResourceUsageMixin,
     BaseStepPart,
 ):
     """Perform SV calling on exomes using Delly2"""

snappy_pipeline/workflows/common/manta.py

@@ -18,10 +18,10 @@
 
 
 class MantaStepPart(
+    SvCallingGetLogFileMixin,
+    SvCallingGetResultFilesMixin,
     ForwardSnakemakeFilesMixin,
     ForwardResourceUsageMixin,
-    SvCallingGetResultFilesMixin,
-    SvCallingGetLogFileMixin,
     BaseStepPart,
 ):
     """Perform SV calling on exomes using Manta"""
@@ -56,13 +56,13 @@ def _get_input_files_run(self, wildcards):
 
     @dictify
     def _get_output_files_run(self):
-        infix = "{mapper}.delly2.{library_name}"
+        infix = "{mapper}.manta.{library_name}"
         work_files = {
             "vcf": f"work/{infix}/out/{infix}.vcf.gz",
             "vcf_md5": f"work/{infix}/out/{infix}.vcf.gz.md5",
             "vcf_tbi": f"work/{infix}/out/{infix}.vcf.gz.tbi",
             "vcf_tbi_md5": f"work/{infix}/out/{infix}.vcf.gz.tbi.md5",
         }
         yield from augment_work_dir_with_output_links(
-            work_files, self.get_log_file("merge_genotypes").values()
+            work_files, self.get_log_file().values()
         ).items()

snappy_pipeline/workflows/common/sv_calling.py

@@ -1,5 +1,7 @@
 """Code shared by steps in ``sv_calling_{targeted,wgs}``"""
 
+import typing
+
 from snakemake.io import expand
 
 from snappy_pipeline.utils import DictQuery, dictify, flatten, listify
@@ -15,6 +17,9 @@ def get_result_files(self):
         The implementation will return a list of all paths with prefix ``output/` that are
         returned by ``self.get_output_files()`` for all actions in ``self.actions``.
         """
+        if self.name not in DictQuery(self.w_config).get(f"step_config/{self.parent.name}/tools"):
+            return  # tool not enabled, no result files
+
         ngs_mapping_config = DictQuery(self.w_config).get("step_config/ngs_mapping")
         for mapper in ngs_mapping_config["tools"]["dna"]:
             # Get list of result path templates.
@@ -39,13 +44,13 @@ class SvCallingGetLogFileMixin:
     """Mixin that provides ``get_log_files()`` for SV calling steps"""
 
     @dictify
-    def get_log_file(self, action):
+    def get_log_file(self, action: typing.Optional[str] = None):
         """Return dict of log files in the "log" directory"""
         _ = action
-        if action != "merge_genotypes":
-            infix = f"delly2_{action}"
+        if action and action != self.actions[-1]:
+            infix = f"{self.name}_{action}"
         else:
-            infix = "delly2"
+            infix = self.name
         prefix = f"work/{{mapper}}.{infix}.{{library_name}}/log/{{mapper}}.{infix}.{{library_name}}.sv_calling"
         key_ext = (
             ("log", ".log"),

snappy_pipeline/workflows/sv_calling_wgs/__init__.py

@@ -243,10 +243,10 @@ def get_ped_members(self, wildcards):
 
 
 class MeltStepPart(
-    ForwardSnakemakeFilesMixin,
-    ForwardResourceUsageMixin,
     SvCallingGetResultFilesMixin,
     SvCallingGetLogFileMixin,
+    ForwardSnakemakeFilesMixin,
+    ForwardResourceUsageMixin,
     BaseStepPart,
 ):
     """MEI calling using MELT

tests/snappy_pipeline/workflows/test_workflows_sv_calling_targeted.py

@@ -39,6 +39,8 @@ def minimal_config():
 
           sv_calling_targeted:
             tools:
+              - delly2
+              - manta
               - gcnv
             path_target_interval_list_mapping:
               - pattern: "Agilent SureSelect Human All Exon V6.*"
@@ -313,18 +315,6 @@ def test_target_seq_cnv_calling_workflow_all_donors(
         assert donor.dna_ngs_library.name in expected, msg
 
 
-def test_target_seq_cnv_calling_workflow_all_background_donors(
-    sv_calling_targeted_workflow, sv_calling_targeted_workflow_large_cohort_background
-):
-    """Tests SvCallingTargetedWorkflow.all_background_donors()"""
-    # Test small foreground sample sheet
-    actual = sv_calling_targeted_workflow.all_background_donors()
-    assert len(actual) == 0, "Small sample sheet should contain zero background donors."
-    # Test large background sample sheet
-    actual = sv_calling_targeted_workflow_large_cohort_background.all_background_donors()
-    assert len(actual) == 501, "Large sample sheet should contain 501 background donors."
-
-
 def test_target_seq_cnv_calling_workflow_get_library_count(sv_calling_targeted_workflow):
     """Tests SvCallingTargetedWorkflow.get_library_count()"""
     # Test undefined library kit