fix(cpg_flow_test/,cpg_flow_test/jobs/): fix dependency in first stage

populationgenomics · Dec 13, 2024 · 9256c68 · 9256c68
1 parent 7efab1c
commit 9256c68
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Showing 3 changed files with 5 additions and 8 deletions.
diff --git a/cpg_flow_test/jobs/first_n_primes.py b/cpg_flow_test/jobs/first_n_primes.py
@@ -3,15 +3,14 @@
 from hailtop.batch.job import Job
 
 
-def first_n_primes(
-    b: Batch,
-    input_file_path: str,
-    output_file_path: str,
-) -> list[Job]:
+def first_n_primes(b: Batch, input_file_path: str, output_file_path: str, depends_on: Job) -> list[Job]:
     title = 'First N Primes'
     job = b.new_job(name=title)
     id_sum_path = b.read_input(input_file_path)
 
+    if depends_on:
+        job.depends_on(depends_on)
+
     cmd = f"""
     is_prime() {{
         local num=$1

diff --git a/cpg_flow_test/jobs/iterative_digit_sum.py b/cpg_flow_test/jobs/iterative_digit_sum.py
@@ -42,8 +42,6 @@ def iterative_digit_sum(
         iterative_digit_sum "$concatenated_digits"
         }}
 
-        # Example usage
-        # Replace "$1" with your actual input
         echo "Input: {sequencing_group.id}\n"
         result=$(extract_digits_and_sum {sequencing_group.id})
         echo "Result: $result\n"

diff --git a/cpg_flow_test/stages.py b/cpg_flow_test/stages.py
@@ -71,7 +71,7 @@ def queue_jobs(self, sequencing_group: SequencingGroup, inputs: StageInput) -> S
 
         # Generate first N primes
         primes_output_path = str(self.expected_outputs(sequencing_group).get('primes', ''))
-        job_primes = first_n_primes(b, id_sum_output_path, primes_output_path)
+        job_primes = first_n_primes(b, id_sum_output_path, primes_output_path, depends_on=job_id_sum)
 
         jobs = [job_id_sum, job_primes]