From b54741ee4656df31e412d8cc38f1f9376e07db35 Mon Sep 17 00:00:00 2001
From: chaopower <chao.zhang@jmdna.com>
Date: Tue, 26 Dec 2023 16:35:05 +0800
Subject: [PATCH] bug

---
 codes/cromwell.examples.conf | 14 +++++++-------
 codes/run_wdl.py             |  4 ++--
 pipeline.wdl                 |  4 ----
 wdl/pollution.wdl            |  1 -
 4 files changed, 9 insertions(+), 14 deletions(-)

diff --git a/codes/cromwell.examples.conf b/codes/cromwell.examples.conf
index 8dd5d60..326a87f 100755
--- a/codes/cromwell.examples.conf
+++ b/codes/cromwell.examples.conf
@@ -39,16 +39,16 @@ system {
   # 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.
   # 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
   max-concurrent-workflows = 10000
 
   # 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
-  #new-workflow-poll-rate = 20
+  new-workflow-poll-rate = 20
 
   # Since the WorkflowLogCopyRouter is initialized in code, this is the number of workers
   #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.
 
     # 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.
     # 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 {
       enabled: true
       # Guava cache concurrency.
-      concurrency: 1
+      concurrency: 10
       # How long entries in the cache should live from the time they are added to the cache.
       ttl: 10 minutes
       # 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
-  dns-cache-ttl: 3 minutes
+  dns-cache-ttl: 30 minutes
 }
 
 workflow-options {
@@ -286,7 +286,7 @@ languages {
             #     # How long entries in the cache should live from the time of their last access.
             ttl: 20 minutes
             #     # Maximum number of entries in the cache (i.e. the number of workflow source + imports => namespace entries).
-            size: 10000
+            size: 100000
           }
         }
       }
diff --git a/codes/run_wdl.py b/codes/run_wdl.py
index 214f6a5..2c732ba 100755
--- a/codes/run_wdl.py
+++ b/codes/run_wdl.py
@@ -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'-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'-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'{cmd3}; {cmd4}'
 
diff --git a/pipeline.wdl b/pipeline.wdl
index b341c7d..30a3e0b 100644
--- a/pipeline.wdl
+++ b/pipeline.wdl
@@ -209,8 +209,4 @@ workflow pipeline {
             cancer=cancer,
             project=project
     }
-
-    output {
-        String result = "${output_dir}/report/${tumor}.merged_file.xlsx"
-    }
 }
\ No newline at end of file
diff --git a/wdl/pollution.wdl b/wdl/pollution.wdl
index 737cf8f..b548e47 100755
--- a/wdl/pollution.wdl
+++ b/wdl/pollution.wdl
@@ -1,4 +1,3 @@
-
 task run_pollution {
     String name
     String output_dir