all validations

Author: bpblanken

v03_pipeline/lib/tasks/validate_callset.py

@@ -3,6 +3,7 @@
 import luigi.util
 
 from v03_pipeline.lib.misc.validation import (
+    ALL_VALIDATIONS,
     SKIPPABLE_VALIDATIONS,
     SeqrValidationError,
 )
@@ -31,7 +32,8 @@ class ValidateCallsetTask(BaseUpdateTask):
     def validation_dependencies(self) -> dict[str, hl.Table]:
         deps = {}
         if (
-            'validate_sample_type' not in self.validations_to_skip
+            ALL_VALIDATIONS not in self.validations_to_skip
+            and 'validate_sample_type' not in self.validations_to_skip
             and self.dataset_type.can_run_validation
         ):
             deps['coding_and_noncoding_variants_ht'] = hl.read_table(
@@ -62,7 +64,8 @@ def output(self) -> luigi.Target:
     def requires(self) -> list[luigi.Task]:
         requirements = [self.clone(WriteImportedCallsetTask)]
         if (
-            'validate_sample_type' not in self.validations_to_skip
+            ALL_VALIDATIONS not in self.validations_to_skip
+            and 'validate_sample_type' not in self.validations_to_skip
             and self.dataset_type.can_run_validation
         ):
             requirements = [
@@ -101,7 +104,10 @@ def update_table(self, mt: hl.MatrixTable) -> hl.MatrixTable:
                 ),
             )
 
-        if not self.dataset_type.can_run_validation:
+        if (
+            ALL_VALIDATIONS in self.validations_to_skip
+            or not self.dataset_type.can_run_validation
+        ):
             return mt.select_globals(
                 callset_path=self.callset_path,
                 validated_sample_type=self.sample_type.value,