feat: (#405) somatic variant qc

snappy_pipeline/workflows/somatic_variant_checking/__init__.py

@@ -4,7 +4,6 @@
 from biomedsheets.shortcuts import CancerCaseSheet, CancerCaseSheetOptions, is_not_background
 from snakemake.io import expand
 
-from snappy_pipeline.base import UnsupportedActionException
 from snappy_pipeline.utils import dictify, listify
 from snappy_pipeline.workflows.abstract import BaseStep, BaseStepPart, LinkOutStepPart
 from snappy_pipeline.workflows.ngs_mapping import NgsMappingWorkflow, ResourceUsage
@@ -27,10 +26,11 @@
         tools_ngs_mapping: []      # default to those configured for ngs_mapping
         tools_somatic_variant_calling: []  # default to those configured for somatic_variant_calling
         target_regions: # REQUIRED
-        padding: 0  #Used for count the number of variants outside of exom + padding
-        ignore_regions: []
-        minimal_support_read: 1
-        limited_support_read: 5
+        padding: 0  # Used for count the number of variants outside of exom + padding
+        AF_ID: 'AF' # REQUIRED ID of allele frequency field used in vcf file
+        ignore_regions: "" # hard mapping regions
+        minimal_support_read: 1 # threshold for defining a variant that has minimal support reads
+        limited_support_read: 5 # threshold for defining a variant that has limited support reads
 """
 
 
@@ -76,7 +76,7 @@ def get_output_files(self, action):
 
     @dictify
     def _get_log_file(self, action):
-        assert action == "run"
+        self._validate_action(action=action)
         prefix = (
             "work/{mapper}.{var_caller}.variantsqc.{tumor_library}/log/"
             "{mapper}.{var_caller}.variantsqc.{tumor_library}"
@@ -97,10 +97,7 @@ def get_resource_usage(self, action):
         :return: Returns ResourceUsage for step.
         :raises UnsupportedActionException: if action not in class defined list of valid actions.
         """
-        if action not in self.actions:
-            actions_str = ", ".join(self.actions)
-            error_message = f"Action '{action}' is not supported. Valid options: {actions_str}"
-            raise UnsupportedActionException(error_message)
+        self._validate_action(action=action)
         mem_mb = 4 * 1024  # 4GB
         return ResourceUsage(
             threads=2,
@@ -189,10 +186,7 @@ def _yield_result_files_matched(self, tpl, **kwargs):
         """
         for sheet in filter(is_not_background, self.shortcut_sheets):
             for sample_pair in sheet.all_sample_pairs:
-                if (
-                    not sample_pair.tumor_sample.dna_ngs_library
-                    or not sample_pair.normal_sample.dna_ngs_library
-                ):
+                if not sample_pair.tumor_sample.dna_ngs_library:
                     msg = (
                         "INFO: sample pair for cancer bio sample {} has is missing primary"
                         "normal or primary cancer NGS library"

snappy_pipeline/workflows/tumor_mutational_burden/__init__.py

@@ -5,10 +5,14 @@
 from biomedsheets.shortcuts import CancerCaseSheet, CancerCaseSheetOptions, is_not_background
 from snakemake.io import expand
 
-from snappy_pipeline.base import UnsupportedActionException
 from snappy_pipeline.utils import dictify, listify
-from snappy_pipeline.workflows.abstract import BaseStep, BaseStepPart, LinkOutStepPart
-from snappy_pipeline.workflows.ngs_mapping import NgsMappingWorkflow, ResourceUsage
+from snappy_pipeline.workflows.abstract import (
+    BaseStep,
+    BaseStepPart,
+    LinkOutStepPart,
+    ResourceUsage,
+)
+from snappy_pipeline.workflows.ngs_mapping import NgsMappingWorkflow
 from snappy_pipeline.workflows.somatic_variant_calling import (
     SOMATIC_VARIANT_CALLERS_MATCHED,
     SomaticVariantCallingWorkflow,
@@ -80,7 +84,7 @@ def get_output_files(self, action):
 
     @dictify
     def _get_log_file(self, action):
-        assert action == "run"
+        self._validate_action(action)
         prefix = (
             "work/{mapper}.{var_caller}.tmb.{tumor_library}/log/"
             "{mapper}.{var_caller}.tmb.{tumor_library}"
@@ -101,10 +105,7 @@ def get_resource_usage(self, action):
         :return: Returns ResourceUsage for step.
         :raises UnsupportedActionException: if action not in class defined list of valid actions.
         """
-        if action not in self.actions:
-            actions_str = ", ".join(self.actions)
-            error_message = f"Action '{action}' is not supported. Valid options: {actions_str}"
-            raise UnsupportedActionException(error_message)
+        self._validate_action(action)
         mem_mb = 4 * 1024  # 4GB
         return ResourceUsage(
             threads=2,