Add protection against a user supplying the wrong sample type on a re-run. (#673)

* Add sample type to callset to ensure that it was supplied correctly

* add sample type to imported callset

* correct method

* string fixes

* hasattr

* Fix syntax

Author: bpblanken

v03_pipeline/lib/tasks/write_imported_callset.py

@@ -31,6 +31,12 @@ class WriteImportedCallsetTask(BaseWriteTask):
         parsing=luigi.BoolParameter.EXPLICIT_PARSING,
     )
 
+    def complete(self) -> luigi.Target:
+        if super().complete():
+            mt = hl.read_matrix_table(self.output().path)
+            return hasattr(mt, 'sample_type') and hl.eval(self.sample_type.value == mt.sample_type)
+        return False
+
     def output(self) -> luigi.Target:
         return GCSorLocalTarget(
             imported_callset_path(
@@ -97,4 +103,6 @@ def create_table(self) -> hl.MatrixTable:
                 self.reference_genome,
                 self.sample_type,
             )
-        return mt
+        return mt.annotate_globals(
+            sample_type=self.sample_type.value,
+        )