test(filter_evens.py,cpg_flow_test/stages.py): print inputs

populationgenomics · Dec 13, 2024 · 9347dd2 · 9347dd2
1 parent 454b2a3
commit 9347dd2
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diff --git a/cpg_flow_test/jobs/filter_evens.py b/cpg_flow_test/jobs/filter_evens.py
@@ -1,12 +1,15 @@
 from typing import Any
 
+from cpg_flow.stage import Stage, StageInput
 from cpg_flow.targets.sequencing_group import SequencingGroup
 from hailtop.batch import Batch
 from hailtop.batch.job import Job
 
 
 def filter_evens(
     b: Batch,
+    inputs: StageInput,
+    previous_stage: Stage,
     sequencing_groups: list[SequencingGroup],
     input_files: dict[str, dict[str, Any]],
     sg_outputs: dict[str, dict[str, Any]],
@@ -20,6 +23,7 @@ def filter_evens(
     for sg in sequencing_groups:  # type: ignore
         job = b.new_job(name=title + ': ' + sg.id)
         input_file_path = input_files[sg.id]['cumulative']
+        input_file_path = inputs.as_path(sg, previous_stage, 'cumulative')
         no_evens_input_file = b.read_input(input_file_path)
         no_evens_output_file_path = str(sg_outputs[sg.id])
         sg_output_files.append(no_evens_output_file_path)

diff --git a/cpg_flow_test/stages.py b/cpg_flow_test/stages.py
@@ -117,9 +117,14 @@ def queue_jobs(self, cohort: Cohort, inputs: StageInput) -> StageOutput | None:
         input_files = inputs.as_dict_by_target(CumulativeCalc)
         b = get_batch()
 
+        print('-----INPUTS-----')
+        print(inputs)
+
         sg_outputs = self.expected_outputs(cohort)
         no_evens_output_path = str(sg_outputs['no_evens'])
-        job_no_evens = filter_evens(b, cohort.get_sequencing_groups(), input_files, sg_outputs, no_evens_output_path)
+        job_no_evens = filter_evens(
+            b, inputs, CumulativeCalc, cohort.get_sequencing_groups(), input_files, sg_outputs, no_evens_output_path,
+        )
 
         jobs = [job_no_evens]