Non pre-emptible gVCF combiner jobs

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.32.12
+current_version = 1.32.13
 commit = True
 tag = False
 

.github/workflows/docker.yaml

@@ -15,7 +15,7 @@ permissions:
   contents: read
 
 env:
-  VERSION: 1.32.12
+  VERSION: 1.32.13
 
 jobs:
   docker:

configs/defaults/rd_combiner.toml

@@ -49,6 +49,8 @@ driver_storage = "10Gi"
 driver_cores = 1
 # highem, standard, or a string, e.g. "4Gi"
 worker_memory = "standard"
+# if false, use non-preemptible VMs
+preemptible_vms = false
 
 [vqsr]
 # VQSR, when applying model, targets indel_filter_level and snp_filter_level

cpg_workflows/stages/rd_combiner.py

@@ -173,6 +173,10 @@ def queue_jobs(self, multicohort: MultiCohort, inputs: StageInput) -> StageOutpu
         combiner_job.storage(config_retrieve(['combiner', 'driver_storage']))
         combiner_job.cpu(config_retrieve(['combiner', 'driver_cores'], 2))
 
+        # set this job to be non-spot (i.e. non-preemptible)
+        # previous issues with preemptible VMs led to multiple simultaneous QOB groups processing the same data
+        combiner_job.spot(config_retrieve(['combiner', 'preemptible_vms'], False))
+
         # Default to GRCh38 for reference if not specified
         combiner_job.call(
             combiner.run,

setup.py

@@ -5,7 +5,7 @@
 setup(
     name='cpg_workflows',
     # This tag is automatically updated by bumpversion
-    version='1.32.12',
+    version='1.32.13',
     description='CPG workflows for Hail Batch',
     long_description=open('README.md').read(),
     long_description_content_type='text/markdown',