more hacking

Author: bpblanken

v03_pipeline/lib/tasks/write_metadata_for_run.py

@@ -2,40 +2,23 @@
 
 import hail as hl
 import luigi
+import luigi.util
 
 from v03_pipeline.lib.misc.callsets import callset_project_pairs
-from v03_pipeline.lib.model import SampleType
 from v03_pipeline.lib.paths import metadata_for_run_path
 from v03_pipeline.lib.tasks.base.base_hail_table import BaseHailTableTask
+from v03_pipeline.lib.tasks.base.base_loading_run_params import BaseLoadingRunParams
 from v03_pipeline.lib.tasks.files import GCSorLocalTarget
 from v03_pipeline.lib.tasks.write_remapped_and_subsetted_callset import (
     WriteRemappedAndSubsettedCallsetTask,
 )
 
 
+@luigi.util.inherits(BaseLoadingRunParams)
 class WriteMetadataForRunTask(BaseHailTableTask):
-    sample_type = luigi.EnumParameter(enum=SampleType)
-    callset_paths = luigi.ListParameter()
     project_guids = luigi.ListParameter()
     project_remap_paths = luigi.ListParameter()
     project_pedigree_paths = luigi.ListParameter()
-    imputed_sex_paths = luigi.ListParameter(default=None)
-    ignore_missing_samples_when_remapping = luigi.BoolParameter(
-        default=False,
-        parsing=luigi.BoolParameter.EXPLICIT_PARSING,
-    )
-    validate = luigi.BoolParameter(
-        default=True,
-        parsing=luigi.BoolParameter.EXPLICIT_PARSING,
-    )
-    force = luigi.BoolParameter(
-        default=False,
-        parsing=luigi.BoolParameter.EXPLICIT_PARSING,
-    )
-    check_sex_and_relatedness = luigi.BoolParameter(
-        default=True,
-        parsing=luigi.BoolParameter.EXPLICIT_PARSING,
-    )
     run_id = luigi.Parameter()
 
     def output(self) -> luigi.Target:
@@ -52,7 +35,7 @@ def complete(self) -> bool:
 
     def requires(self) -> list[luigi.Task]:
         return [
-            WriteRemappedAndSubsettedCallsetTask(
+            self.clone(WriteRemappedAndSubsettedCallsetTask,
                 self.reference_genome,
                 self.dataset_type,
                 self.sample_type,

v03_pipeline/lib/tasks/write_remapped_and_subsetted_callset.py

@@ -30,6 +30,10 @@
 
 @luigi.util.inherits(BaseLoadingRunParams)
 class WriteRemappedAndSubsettedCallsetTask(BaseWriteTask):
+    project_guid = luigi.Parameter()
+    project_remap_path = luigi.Parameter()
+    project_pedigree_path = luigi.Parameter()
+
     def complete(self) -> luigi.Target:
         return not self.force and super().complete()