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bug

master
chaopower 2023-12-26 16:35:05 +08:00
parent ac08a562d0
commit b54741ee46
4 changed files with 9 additions and 14 deletions
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14
codes/cromwell.examples.conf
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@ -39,16 +39,16 @@ system {
# If 'true', a SIGTERM or SIGINT will trigger Cromwell to attempt to gracefully shutdown in server mode, # If 'true', a SIGTERM or SIGINT will trigger Cromwell to attempt to gracefully shutdown in server mode,
# in particular clearing up all queued database writes before letting the JVM shut down. # in particular clearing up all queued database writes before letting the JVM shut down.
# The shutdown is a multi-phase process, each phase having its own configurable timeout. See the Dev Wiki for more details. # The shutdown is a multi-phase process, each phase having its own configurable timeout. See the Dev Wiki for more details.
graceful-server-shutdown = true graceful-server-shutdown = false
# Cromwell will cap the number of running workflows at N # Cromwell will cap the number of running workflows at N
max-concurrent-workflows = 10000 max-concurrent-workflows = 10000
# Cromwell will launch up to N submitted workflows at a time, regardless of how many open workflow slots exist # Cromwell will launch up to N submitted workflows at a time, regardless of how many open workflow slots exist
max-workflow-launch-count = 100 max-workflow-launch-count = 1000
# Number of seconds between workflow launches # Number of seconds between workflow launches
#new-workflow-poll-rate = 20 new-workflow-poll-rate = 20
# Since the WorkflowLogCopyRouter is initialized in code, this is the number of workers # Since the WorkflowLogCopyRouter is initialized in code, this is the number of workers
#number-of-workflow-log-copy-workers = 10 #number-of-workflow-log-copy-workers = 10
@ -95,7 +95,7 @@ system {
# These are the default values in Cromwell, in most circumstances there should not be a need to change them. # These are the default values in Cromwell, in most circumstances there should not be a need to change them.
# How frequently Cromwell should scan for aborts. # How frequently Cromwell should scan for aborts.
scan-frequency: 30 seconds scan-frequency: 600 seconds
# The cache of in-progress aborts. Cromwell will add entries to this cache once a WorkflowActor has been messaged to abort. # The cache of in-progress aborts. Cromwell will add entries to this cache once a WorkflowActor has been messaged to abort.
# If on the next scan an 'Aborting' status is found for a workflow that has an entry in this cache, Cromwell will not ask # If on the next scan an 'Aborting' status is found for a workflow that has an entry in this cache, Cromwell will not ask
@ -103,7 +103,7 @@ system {
cache { cache {
enabled: true enabled: true
# Guava cache concurrency. # Guava cache concurrency.
concurrency: 1 concurrency: 10
# How long entries in the cache should live from the time they are added to the cache. # How long entries in the cache should live from the time they are added to the cache.
ttl: 10 minutes ttl: 10 minutes
# Maximum number of entries in the cache. # Maximum number of entries in the cache.
@ -112,7 +112,7 @@ system {
} }
# Cromwell reads this value into the JVM's `networkaddress.cache.ttl` setting to control DNS cache expiration # Cromwell reads this value into the JVM's `networkaddress.cache.ttl` setting to control DNS cache expiration
dns-cache-ttl: 3 minutes dns-cache-ttl: 30 minutes
} }
workflow-options { workflow-options {
@ -286,7 +286,7 @@ languages {
# # How long entries in the cache should live from the time of their last access. # # How long entries in the cache should live from the time of their last access.
ttl: 20 minutes ttl: 20 minutes
# # Maximum number of entries in the cache (i.e. the number of workflow source + imports => namespace entries). # # Maximum number of entries in the cache (i.e. the number of workflow source + imports => namespace entries).
size: 10000 size: 100000
} }
} }
} }

4
codes/run_wdl.py
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@ -94,9 +94,9 @@ def run(barcode, normal, umi, input_dir, output_dir, project, cancer, probe, wdl
# f'{"-Dcall-caching.enabled=false " if uncache else ""}' # f'{"-Dcall-caching.enabled=false " if uncache else ""}'
# f'-Dconfig.file=/home/zhangchao/project/pipeline/workflow/script/cromwell.examples.conf ' \ # f'-Dconfig.file=/home/zhangchao/project/pipeline/workflow/script/cromwell.examples.conf ' \
cmd4 = f'/home/install/product/workflow/software/jdk-17.0.7+7/bin/java ' \ cmd4 = f'/home/install/product/workflow/software/jdk-17.0.7+7/bin/java -DLOG_MODE=standard ' \
f'-Dconfig.file=$WORKFLOW/codes/cromwell.examples.conf ' \ f'-Dconfig.file=$WORKFLOW/codes/cromwell.examples.conf ' \
f'-jar $WORKFLOW/software/cromwell-86.jar run {wdl} --inputs {jsfile_path} --metadata-output run.log' f'-jar $WORKFLOW/software/cromwell-86.jar run {wdl} --inputs {jsfile_path} '
# cmd = f'{cmd1}; {cmd2}; {cmd3}; {cmd4}' # cmd = f'{cmd1}; {cmd2}; {cmd3}; {cmd4}'
cmd = f'{cmd3}; {cmd4}' cmd = f'{cmd3}; {cmd4}'

4
pipeline.wdl
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@ -209,8 +209,4 @@ workflow pipeline {
cancer=cancer, cancer=cancer,
project=project project=project
} }
output {
String result = "${output_dir}/report/${tumor}.merged_file.xlsx"
}
} }

1
wdl/pollution.wdl
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@ -1,4 +1,3 @@
task run_pollution { task run_pollution {
String name String name
String output_dir String output_dir