Created
December 9, 2018 19:16
-
-
Save chapmanb/93d5468ac691012eaf70e67c17ed2498 to your computer and use it in GitHub Desktop.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
include required(classpath("application")) | |
system { | |
workflow-restart = true | |
} | |
call-caching { | |
enabled = true | |
} | |
load-control { | |
# Avoid watching memory, since the load-controller stops jobs on local runs | |
memory-threshold-in-mb = 1 | |
} | |
cwltool-runner { | |
# Use external cwltool to avoid slow runtimes with java embedded pre-processing | |
class = "cwl.CwltoolProcess" | |
} | |
database { | |
profile = "slick.jdbc.HsqldbProfile$" | |
db { | |
driver = "org.hsqldb.jdbcDriver" | |
url = "jdbc:hsqldb:file:/home/chapmanb/drive/work/cwl/test_bcbio_cwl/gcp/cromwell_work/persist/metadata;shutdown=false;hsqldb.tx=mvcc" | |
connectionTimeout = 200000 | |
} | |
} | |
google { | |
application-name = "cromwell" | |
auths = [ | |
{ | |
name = "gcp-auth" | |
scheme = "service_account" | |
json-file = ${?GOOGLE_APPLICATION_CREDENTIALS} | |
} | |
] | |
} | |
engine { | |
filesystems { | |
gcs { | |
auth = "gcp-auth" | |
project = "somatic-validation" | |
} | |
} | |
} | |
backend { | |
providers { | |
Local { | |
config { | |
concurrent-job-limit = 1 | |
runtime-attributes = """ | |
Int? cpu | |
Int? memory_mb | |
String? docker | |
String? docker_user | |
Int? cpuMin | |
Int? cpuMax | |
Int? memoryMin | |
Int? memoryMax | |
String? outDirMin | |
String? outDirMax | |
String? tmpDirMin | |
String? tmpDirMax | |
""" | |
filesystems { | |
gcs { | |
auth = "gcp-auth" | |
caching { | |
duplication-strategy = "copy" | |
} | |
} | |
} | |
} | |
} | |
PAPI { | |
actor-factory = "cromwell.backend.google.pipelines.v2alpha1.PipelinesApiLifecycleActorFactory" | |
config { | |
project = "somatic-validation" | |
root = "gs://bcbiotest/gcp/work_cromwell" | |
genomics { | |
auth = "gcp-auth" | |
endpoint-url = "https://genomics.googleapis.com/" | |
} | |
filesystems { | |
gcs { | |
auth = "gcp-auth" | |
project = "somatic-validation" | |
} | |
} | |
} | |
} | |
} | |
} |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment