revert housekeeping

cpg_workflows/stages/gcnv.py

@@ -356,7 +356,7 @@ def queue_jobs(self, cohort: Cohort, inputs: StageInput) -> StageOutput:
                 get_logger().info(f'Using XY-trimmed VCF for {sgid}')
                 all_vcfs.append(str(trimmed_vcfs[sgid]))
             elif sgid in cnv_vcfs:
-                get_logger().debug(f'Using standard VCF for {sgid}')
+                get_logger().warning(f'Using standard VCF for {sgid}')
                 all_vcfs.append(str(cnv_vcfs[sgid]['segments']))
             else:
                 raise ValueError(f'No VCF found for {sgid}')

cpg_workflows/stages/seqr_loader.py

@@ -7,26 +7,19 @@
 
 from google.api_core.exceptions import PermissionDenied
 
-from cpg_utils import Path
+from cpg_utils import Path, to_path
 from cpg_utils.cloud import read_secret
 from cpg_utils.config import config_retrieve, get_config, image_path
 from cpg_utils.hail_batch import get_batch, query_command
 from cpg_workflows.jobs.seqr_loader import annotate_dataset_jobs, cohort_to_vcf_job
 from cpg_workflows.query_modules import seqr_loader
-from cpg_workflows.stages.joint_genotyping import JointGenotyping
-from cpg_workflows.stages.vep import Vep
-from cpg_workflows.stages.vqsr import Vqsr
 from cpg_workflows.targets import Dataset, MultiCohort
 from cpg_workflows.utils import get_logger, tshirt_mt_sizing
-from cpg_workflows.workflow import (
-    DatasetStage,
-    MultiCohortStage,
-    StageInput,
-    StageOutput,
-    get_multicohort,
-    get_workflow,
-    stage,
-)
+from cpg_workflows.workflow import DatasetStage, MultiCohortStage, StageInput, StageOutput, get_multicohort, get_workflow, stage
+
+from .joint_genotyping import JointGenotyping
+from .vep import Vep
+from .vqsr import Vqsr
 
 
 @stage(required_stages=[JointGenotyping, Vqsr, Vep])