Merge pull request #746 from broadinstitute/benb/add_logging

add logging

Author: bpblanken

v03_pipeline/lib/tasks/write_remapped_and_subsetted_callset.py

@@ -1,6 +1,7 @@
 import hail as hl
 import luigi
 
+from v03_pipeline.lib.logger import get_logger
 from v03_pipeline.lib.misc.family_loading_failures import (
     get_families_failed_missing_samples,
     get_families_failed_relatedness_check,
@@ -18,6 +19,8 @@
 )
 from v03_pipeline.lib.tasks.write_sex_check_table import WriteSexCheckTableTask
 
+logger = get_logger(__name__)
+
 
 class WriteRemappedAndSubsettedCallsetTask(BaseWriteTask):
     callset_path = luigi.Parameter()
@@ -137,6 +140,14 @@ def create_table(self) -> hl.MatrixTable:
             - families_failed_sex_check.keys()
         )
         if not len(loadable_families):
+            msg = (
+                f'families_failed_missing_samples: {families_failed_missing_samples}\n'
+                f'families_failed_relatedness_check: {families_failed_missing_samples}\n'
+                f'families_failed_sex_check: {families_failed_sex_check}'
+            )
+            logger.info(
+                msg,
+            )
             msg = 'All families failed checks'
             raise RuntimeError(msg)