def sample_loop(job,
bucket_region,
s3_bucket,
uuid_list,
bwa_inputs,
adam_inputs,
gatk_preprocess_inputs,
gatk_adam_call_inputs,
gatk_gatk_call_inputs,
pipeline_to_run,
skip_alignment,
skip_preprocessing,
autoscale_cluster):
"""
Loops over the sample_ids (uuids) in the manifest, creating child jobs to process each
"""
for uuid in uuid_list:
uuid_bwa_inputs = copy.deepcopy(bwa_inputs)
uuid_adam_inputs = copy.deepcopy(adam_inputs)
uuid_gatk_preprocess_inputs = copy.deepcopy(gatk_preprocess_inputs)
uuid_gatk_adam_call_inputs = copy.deepcopy(gatk_adam_call_inputs)
uuid_gatk_gatk_call_inputs = copy.deepcopy(gatk_gatk_call_inputs)
## set uuid inputs
uuid_bwa_inputs['lb'] = uuid
uuid_bwa_inputs['uuid'] = uuid
uuid_adam_inputs['outDir'] = 's3://{s3_bucket}/analysis/{uuid}'.format(**locals())
uuid_adam_inputs['bamName'] = 's3://{s3_bucket}/alignment/{uuid}.bam'.format(**locals())
uuid_gatk_preprocess_inputs['s3_dir'] = '{s3_bucket}/analysis/{uuid}'.format(**locals())
uuid_gatk_adam_call_inputs['s3_dir'] = '{s3_bucket}/analysis/{uuid}'.format(**locals())
uuid_gatk_gatk_call_inputs['s3_dir'] = '{s3_bucket}/analysis/{uuid}'.format(**locals())
# are we autoscaling? if so, bump the cluster size by one now
if autoscale_cluster:
Samples.increase_nodes(uuid, 1)
job.addChildJobFn(static_dag,
bucket_region,
s3_bucket,
uuid,
uuid_bwa_inputs,
uuid_adam_inputs,
uuid_gatk_preprocess_inputs,
uuid_gatk_adam_call_inputs,
uuid_gatk_gatk_call_inputs,
pipeline_to_run,
skip_alignment,
skip_preprocessing,
autoscale_cluster)
def sample_loop(job, uuid_list, inputs):
"""
Loops over the sample_ids (uuids) in the manifest, creating child jobs to process each
"""
for uuid_rg in uuid_list:
uuid_items = uuid_rg.split(',')
uuid = uuid_items[0]
rg_line = None
if len(uuid_items) > 1:
rg_line = uuid_items[1]
# are we autoscaling? if so, bump the cluster size by one now
if inputs.autoscale_cluster:
Samples.increase_nodes(uuid, 1)
job.addChildJobFn(static_dag, uuid, rg_line, inputs)
def decrease_node_count(job, nodes_to_add, uuid):
Samples.decrease_nodes(uuid, nodes_to_add)
