sv_calling_targeted: remove superfluous validation, fix minimal confi…

…g, fakefs

snappy_pipeline/workflows/common/gcnv/gcnv_run.py

@@ -105,9 +105,6 @@ def validate_request(self):
             msg_tpl = "Precomputed model paths must be configured (key: 'precomputed_model_paths')."
             raise InvalidConfiguration(msg_tpl)
         else:
-            # Validate configuration - check if only expected keys are present
-            self.validate_precomputed_model_paths_config(config=path_to_models)
-
             # Check model directories content
             for model in path_to_models:
                 # Validate ploidy-model
@@ -133,46 +130,6 @@ def validate_request(self):
                         )
                         raise InvalidConfiguration(msg_tpl.format(str(model)))
 
-    def validate_precomputed_model_paths_config(self, config):
-        """Validate precomputed model config.
-
-        Evaluates if provided configuration has the following format:
-
-        precomputed_model_paths:
-          - library: "Agilent SureSelect Human All Exon V6"
-            contig_ploidy": /path/to/ploidy-model
-            model_pattern: /path/to/model_*
-
-        :param config: List of precomputed model configuration dictionary.
-        :type config: list
-
-        :raises InvalidConfiguration: if configuration not as expected for
-        ``precomputed_model_paths`` list.
-        """
-        # Initialise variables
-        expected_keys = ("library", "model_pattern", "contig_ploidy")
-        expected_format = (
-            '{\n    "library": "Agilent SureSelect Human All Exon V6"\n'
-            '    "contig_ploidy": /path/to/ploidy-model\n'
-            '    "model_pattern": "/path/to/model_*"\n}'
-        )
-        # Test
-        for model in config:
-            # Test keys
-            n_keys_pass = len(model) == 3
-            keys_pass = all(key in expected_keys for key in model)
-            # Test values
-            values_pass = all(isinstance(value, str) for value in model.values())
-            # Validate
-            if not (n_keys_pass and keys_pass and values_pass):
-                pretty_model = self._pretty_print_config(config=model)
-                msg = (
-                    "Provided configuration not as expected...\n"
-                    f"\nn_keys_pass={n_keys_pass}, keys_pass={keys_pass}, values_pass={values_pass}\n"
-                    f"Expected:\n{expected_format}\nObserved:\n{pretty_model}\n"
-                )
-                raise InvalidConfiguration(msg)
-
     def _pretty_print_config(self, config):
         """Pretty format configuration.
 

snappy_pipeline/workflows/sv_calling_targeted/model.py

@@ -25,6 +25,8 @@ class Gcnv(SnappyModel):
        path: "path/to/targets.bed"
     """
 
+    path_uniquely_mapable_bed: str
+
     precomputed_model_paths: list[PrecomputedModelEntry] = []
     """
     Path to gCNV model - will execute analysis in CASE MODE.
@@ -92,7 +94,7 @@ class SvCallingTargeted(SnappyStepModel, validators.ToolsMixin):
 
     gcnv: Gcnv | None = None
 
-    dell2: Delly2 | None = None
+    delly2: Delly2 | None = None
 
     manta: Manta | None = None
 

tests/snappy_pipeline/workflows/test_workflows_sv_calling_targeted.py

@@ -40,12 +40,14 @@ def minimal_config():
               - delly2
               - manta
               - gcnv
+            delly2: {}  # use defaults
+            manta: {}   # use defaults
             gcnv:
+              path_uniquely_mapable_bed: /path/to/uniquely/mappable/variable/GRCh37/file.bed.gz
               path_target_interval_list_mapping:
                 - pattern: "Agilent SureSelect Human All Exon V6.*"
                   name: "Agilent_SureSelect_Human_All_Exon_V6"
                   path: /path/to/Agilent/SureSelect_Human_All_Exon_V6_r2/GRCh37/Exons.bed
-                  path_uniquely_mapable_bed: /path/to/uniquely/mappable/variable/GRCh37/file.bed.gz
               precomputed_model_paths:
                 - library: "Agilent SureSelect Human All Exon V6"
                   contig_ploidy: /path/to/ploidy-model
@@ -141,6 +143,7 @@ def sv_calling_targeted_workflow_large_cohort(
     work_dir,
     config_paths,
     germline_sheet_fake_fs2,
+    aligner_indices_fake_fs,
     mocker,
 ):
     """
@@ -149,6 +152,7 @@ def sv_calling_targeted_workflow_large_cohort(
     """
     # Patch out file-system related things in abstract (the crawling link in step is defined there)
     patch_module_fs("snappy_pipeline.workflows.abstract", germline_sheet_fake_fs2, mocker)
+    patch_module_fs("snappy_pipeline.workflows.ngs_mapping", aligner_indices_fake_fs, mocker)
     # Update the "globals" attribute of the mock workflow (snakemake.workflow.Workflow) so we
     # can obtain paths from the function as if we really had a NGSMappingPipelineStep here
     dummy_workflow.globals = {"ngs_mapping": lambda x: "NGS_MAPPING/" + x}
@@ -170,12 +174,14 @@ def sv_calling_targeted_workflow_large_cohort_background(
     work_dir,
     config_paths,
     germline_sheet_fake_fs2,
+    aligner_indices_fake_fs,
     mocker,
 ):
     """Return SvCallingTargetedWorkflow object pre-configured with germline sheet -
     large trio cohort as background."""
     # Patch out file-system related things in abstract (the crawling link in step is defined there)
     patch_module_fs("snappy_pipeline.workflows.abstract", germline_sheet_fake_fs2, mocker)
+    patch_module_fs("snappy_pipeline.workflows.ngs_mapping", aligner_indices_fake_fs, mocker)
     # Update the "globals" attribute of the mock workflow (snakemake.workflow.Workflow) so we
     # can obtain paths from the function as if we really had a NGSMappingPipelineStep here
     dummy_workflow.globals = {"ngs_mapping": lambda x: "NGS_MAPPING/" + x}
@@ -199,13 +205,15 @@ def test_validate_request(
     work_dir,
     config_paths,
     germline_sheet_fake_fs2_gcnv_model,
+    aligner_indices_fake_fs,
     mocker,
 ):
     """Tests SvCallingTargetedWorkflow.validate_request()"""
     # Patch out file-system
     patch_module_fs(
         "snappy_pipeline.workflows.abstract", germline_sheet_fake_fs2_gcnv_model, mocker
     )
+    patch_module_fs("snappy_pipeline.workflows.ngs_mapping", aligner_indices_fake_fs, mocker)
     patch_module_fs(
         "snappy_pipeline.workflows.common.gcnv.gcnv_run",
         germline_sheet_fake_fs2_gcnv_model,
@@ -418,37 +426,6 @@ def test_gcnv_get_params(sv_calling_targeted_workflow):
                 sv_calling_targeted_workflow.get_params("gcnv", action)
 
 
-def test_gcnv_validate_precomputed_model_paths_config(sv_calling_targeted_workflow):
-    """Tests RunGcnvTargetSeqStepPart.validate_model_requirements()"""
-    # Initialise input
-    valid_dict = {
-        "library": "library",
-        "contig_ploidy": "/path/to/ploidy-model",
-        "model_pattern": "/path/to/model_*",
-    }
-    typo_dict = {
-        "library_n": "library",
-        "contig_ploidy": "/path/to/ploidy-model",
-        "model_pattern": "/path/to/model_*",
-    }
-    missing_key_dict = {"model_pattern": "/path/to/model_*"}
-
-    # Sanity check
-    sv_calling_targeted_workflow.substep_getattr("gcnv", "validate_precomputed_model_paths_config")(
-        config=[valid_dict]
-    )
-    # Test key typo
-    with pytest.raises(InvalidConfiguration):
-        sv_calling_targeted_workflow.substep_getattr(
-            "gcnv", "validate_precomputed_model_paths_config"
-        )(config=[valid_dict, typo_dict])
-    # Test key missing
-    with pytest.raises(InvalidConfiguration):
-        sv_calling_targeted_workflow.substep_getattr(
-            "gcnv", "validate_precomputed_model_paths_config"
-        )(config=[valid_dict, missing_key_dict])
-
-
 def test_gcnv_validate_ploidy_model_directory(
     fake_fs, mocker, sv_calling_targeted_workflow, ploidy_model_files
 ):