解决不能自动终止的问题

codes/cromwell.examples.conf

@@ -42,19 +42,19 @@ system {
   graceful-server-shutdown = true
 
   # Cromwell will cap the number of running workflows at N
-  max-concurrent-workflows = 10000
+  max-concurrent-workflows = 5000
 
   # Cromwell will launch up to N submitted workflows at a time, regardless of how many open workflow slots exist
-  max-workflow-launch-count = 1000
+  max-workflow-launch-count = 50
 
   # Number of seconds between workflow launches
-  new-workflow-poll-rate = 20
+  new-workflow-poll-rate = 10
 
   # 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
 
   # Default number of cache read workers
-  #number-of-cache-read-workers = 25
+  number-of-cache-read-workers = 25
 
   io {
     # throttle {
@@ -65,7 +65,7 @@ system {
     # }
 
     # Number of times an I/O operation should be attempted before giving up and failing it.
-    number-of-attempts = 5
+    #number-of-attempts = 5
   }
 
   # Maximum number of input file bytes allowed in order to read each type.
@@ -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: 2 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
@@ -103,16 +103,16 @@ system {
     cache {
       enabled: true
       # Guava cache concurrency.
-      concurrency: 10
+      concurrency: 4
       # How long entries in the cache should live from the time they are added to the cache.
-      ttl: 10 minutes
+      ttl: 20 minutes
       # Maximum number of entries in the cache.
-      size: 200000
+      size: 100000
     }
   }
 
   # Cromwell reads this value into the JVM's `networkaddress.cache.ttl` setting to control DNS cache expiration
-  dns-cache-ttl: 30 minutes
+  dns-cache-ttl: 3 minutes
 }
 
 workflow-options {
@@ -140,7 +140,7 @@ workflow-options {
     workflow-type-version: "draft-2"
 
     # To set a default hog group rather than defaulting to workflow ID:
-    hogGroup: "static"
+    #hogGroup: "static"
   }
 }
 
@@ -148,20 +148,20 @@ workflow-options {
 call-caching {
   # Allows re-use of existing results for jobs you've already run
   # (default: false)
-  enabled = false
+  #enabled = false
 
   # Whether to invalidate a cache result forever if we cannot reuse them. Disable this if you expect some cache copies
   # to fail for external reasons which should not invalidate the cache (e.g. auth differences between users):
   # (default: true)
-  #invalidate-bad-cache-results = true
+  invalidate-bad-cache-results = false
 
   # The maximum number of times Cromwell will attempt to copy cache hits before giving up and running the job.
   #max-failed-copy-attempts = 1000000
 
-  # blacklist-cache {
+   blacklist-cache {
   #   # The call caching blacklist cache is off by default. This cache is used to blacklist cache hits based on cache
   #   # hit ids or buckets of cache hit paths that Cromwell has previously failed to copy for permissions reasons.
-  #   enabled: true
+     enabled: false
   #
   #   # A blacklist grouping can be specified in workflow options which will inform the blacklister which workflows
   #   # should share a blacklist cache.
@@ -170,7 +170,7 @@ call-caching {
   #     concurrency: 10000
   #     ttl: 2 hours
   #     size: 1000
-  #   }
+     }
   #
   #   buckets {
   #     # Guava cache concurrency.
@@ -193,6 +193,58 @@ call-caching {
   # }
 }
 
+# Google configuration
+google {
+
+  #application-name = "cromwell"
+
+  # Default: just application default
+  #auths = [
+
+    # Application default
+    #{
+    #  name = "application-default"
+    #  scheme = "application_default"
+    #},
+
+    # Use a static service account
+    #{
+    #  name = "service-account"
+    #  scheme = "service_account"
+    #  Choose between PEM file and JSON file as a credential format. They're mutually exclusive.
+    #  PEM format:
+    #  service-account-id = "my-service-account"
+    #  pem-file = "/path/to/file.pem"
+    #  JSON format:
+    #  json-file = "/path/to/file.json"
+    #}
+
+    # Use service accounts provided through workflow options
+    #{
+    #   name = "user-service-account"
+    #   scheme = "user_service_account"
+    #}
+  #]
+}
+
+docker {
+  hash-lookup {
+    # Set this to match your available quota against the Google Container Engine API
+    #gcr-api-queries-per-100-seconds = 1000
+
+    # Time in minutes before an entry expires from the docker hashes cache and needs to be fetched again
+    #cache-entry-ttl = "20 minutes"
+
+    # Maximum number of elements to be kept in the cache. If the limit is reached, old elements will be removed from the cache
+    #cache-size = 200
+
+    # How should docker hashes be looked up. Possible values are "local" and "remote"
+    # "local": Lookup hashes on the local docker daemon using the cli
+    # "remote": Lookup hashes on docker hub, gcr, gar, quay
+    #method = "remote"
+  }
+}
+
 engine {
   # This instructs the engine which filesystems are at its disposal to perform any IO operation that it might need.
   # For instance, WDL variables declared at the Workflow level will be evaluated using the filesystems declared here.
@@ -222,21 +274,21 @@ languages {
   WDL {
     versions {
       "draft-2" {
-        language-factory = "languages.wdl.draft2.WdlDraft2LanguageFactory"
+        # language-factory = "languages.wdl.draft2.WdlDraft2LanguageFactory"
-        config {
+        # config {
         #   strict-validation: true
-          enabled: true
+        #   enabled: true
-          caching {
+        #   caching {
         #     # WDL Draft 2 namespace caching is off by default, this value must be set to true to enable it.
-            enabled: true
+        #     enabled: false
         #     # Guava cache concurrency
-            concurrency: 4
+        #     concurrency: 2
         #     # 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).
-            size: 100000
+        #     size: 1000
-          }
+        #   }
-        }
+        # }
       }
       # draft-3 is the same as 1.0 so files should be able to be submitted to Cromwell as 1.0
       # "draft-3" {
@@ -301,7 +353,7 @@ backend {
       config {
 
         # Optional limits on the number of concurrent jobs
-        #concurrent-job-limit = 5
+        concurrent-job-limit = 50
 
         # If true submits scripts to the bash background using "&". Only usefull for dispatchers that do NOT submit
         # the job and then immediately return a scheduled job id.
@@ -321,7 +373,7 @@ backend {
         # `script-epilogue` configures a shell command to run after the execution of every command block.
         #
         # If this value is not set explicitly, the default value is `sync`, equivalent to:
-        # script-epilogue = ""
+        # script-epilogue = "sync"
         #
         # To turn off the default `sync` behavior set this value to an empty string:
         # script-epilogue = ""

codes/run_pipeline.py

@@ -45,7 +45,7 @@ if __name__ == '__main__':
 
     logname = datetime.now().strftime("%m%d%H%M")
 
-    cmd = f'nohup python ' \
+    cmd = f'nohup python3 ' \
           f'{run_wdl_path} -n {args.barcode} -s {args.normal} ' \
           f'{"-u " if args.umi else ""} -i {args.input_dir} ' \
           f'-node {args.start_node} ' \

codes/run_wdl.py

@@ -1,3 +1,5 @@
+#! /usr/bin/env python3
+
 import argparse
 import json
 import os
@@ -87,17 +89,11 @@ def run(barcode, normal, umi, input_dir, output_dir, project, cancer, probe, wdl
         jsfile.write(json.dumps(arg, indent=4, ensure_ascii=False))
 
     # run pipeline
-    # cmd1 = 'export PATH=/home/zhangchao/project/pipeline/workflow/script:$PATH'
-    # cmd2 = 'export PUBLIC=/home/zhangchao/project/pipeline/workflow/script/public'
     cmd3 = f'cd {output_dir}'
 
-    # f'{"-Dcall-caching.enabled=false " if uncache else ""}'
-    # f'-Dconfig.file=/home/zhangchao/project/pipeline/workflow/script/cromwell.examples.conf ' \
-
     cmd4 = f'/usr/bin/java -DLOG_MODE=standard ' \
            f'-Dconfig.file=$WORKFLOW/codes/cromwell.examples.conf ' \
            f'-jar $WORKFLOW/software/cromwell-51.jar run {wdl} --inputs {jsfile_path} '
-    # cmd = f'{cmd1}; {cmd2}; {cmd3}; {cmd4}'
     cmd = f'{cmd3}; {cmd4}'
 
     # 记录开始时间
@@ -107,7 +103,9 @@ def run(barcode, normal, umi, input_dir, output_dir, project, cancer, probe, wdl
     pidnum = ret.pid
     with open(os.path.join(output_dir, 'pid'), 'w') as pidfile:
         pidfile.write(str(pidnum))
-    ret.wait()
+    # ret.wait()
+    # 等待进程完成，并获取输出和错误
+    output, error = ret.communicate()
     # 记录结束时间
     end_time = time.time()
     # 计算运行时间
@@ -115,7 +113,7 @@ def run(barcode, normal, umi, input_dir, output_dir, project, cancer, probe, wdl
 
     print("\n运行时间：{:.2f} 秒".format(elapsed_time))
 
-    print(ret.stdout.read(), ret.stderr.read())
+    print(output, error)
     print('#' * 50)
     print('读取日志')
 

pipeline.wdl

@@ -212,6 +212,6 @@ workflow pipeline {
     }
 
     output {
-        String result = "${output_dir}/report/${tumor}.merged_file.xlsx"
+        String result = call_postprocess.merged
     }
 }

wdl/chemo.wdl

@@ -7,16 +7,17 @@ task run_chemo {
     String vcf
     String cancer
     String project
-    command <<<
+    command {
-
         if [ ! -d ${output_dir}/chemo ];then
         mkdir ${output_dir}/chemo
         fi
 
         chemo.py -d $DATABASE/chemo_database.xlsx -probe ${probe} -n ${name} -v ${vcf} -o ${output_dir}/chemo -c ${cancer} -p ${project}
 
-    >>>
+    }
-
+    output {
+        String chemo_res = "${output_dir}/chemo/${name}.drug.res.txt"
+    }
 }
 
 workflow call_chemo {

wdl/hereditary.wdl

@@ -5,7 +5,7 @@ task run_hereditary {
     String output_dir
     String project
     String filter_txt
-    command <<<
+    command {
 
         if [ ! -d ${output_dir}/hereditary ];then
         mkdir ${output_dir}/hereditary
@@ -13,7 +13,11 @@ task run_hereditary {
 
         hereditary.py -d $DATABASE/hereditary_database.xlsx -p ${project} -n ${name} -f ${filter_txt} -o ${output_dir}/hereditary
 
-    >>>
+    }
+
+    output {
+        String hereditary_txt = "${output_dir}/hereditary/${name}.hereditary.txt"
+    }
 
 }
 

wdl/neoantigen.wdl

@@ -151,6 +151,10 @@ task run_neoantigen {
 
     >>>
 
+    output {
+        String neoantigen_txt = "${output_dir}neoantigen/MHC_Class_I/neoantigen.txt"
+    }
+
 }
 
 workflow call_neoantigen {

wdl/pollution.wdl

@@ -7,7 +7,7 @@ task run_pollution {
     String vcf
     String? vcf2
 
-    command <<<
+    command {
 
         if [ ! -d ${output_dir}/pollution ];then
         mkdir ${output_dir}/pollution
@@ -20,7 +20,7 @@ task run_pollution {
         -b $PUBLIC/pollution/${probe}_contaminate_ref.bed \
         -c $PUBLIC/pollution/${probe}_contaminate_cnvkit.bed
 
-    >>>
+    }
 }
 
 workflow call_pollution {

wdl/postprocess.wdl

@@ -16,17 +16,19 @@ task run_post {
     String cancer
     String project
 
-    command <<<
+    command {
-
         if [ ! -d ${output_dir}/report ];then
         mkdir ${output_dir}/report
         fi
         indication.pl ${output_dir} ${cancer} ${project}
         sample_post.py -s ${name} -o ${output_dir}
         postprocess.py -n ${name} -s ${normal} -c ${output_dir} -o ${output_dir}/report/${name}.merged_file.xlsx
+        sleep 2m
 
-    >>>
+    }
-
+    output {
+        String merged = "${output_dir}/report/${name}.merged_file.xlsx"
+    }
 }
 
 workflow call_postprocess {

wdl/statistics.wdl

@@ -8,7 +8,7 @@ task run_statistics {
     String ref
     String bed
 
-    command <<<
+    command {
 
         if [ ! -d ${output_dir}/qc/${name}_bamdst ];then
         mkdir -p ${output_dir}/qc/${name}_bamdst
@@ -23,7 +23,7 @@ task run_statistics {
         #        ${output_dir}/qc/${name}_InsertAndDepthStat \
         #        ${output_dir}/qc/${name}_bamdst/insertsize.plot \
         #        ${output_dir}/qc/${name}_bamdst/depth_distribution.plot
-    >>>
+    }
 }
 
 workflow statistics {

wdl/tmb.wdl

@@ -7,8 +7,7 @@ task run_tmb {
     String sample_type
     String output_dir
 
-    command <<<
+    command {
-
         if [ ! -d ${output_dir}/tmb ];then
         mkdir ${output_dir}/tmb
         fi
@@ -19,10 +18,14 @@ task run_tmb {
         ${project} \
         ${sample_type} \
         tmb
-    >>>
 
     }
 
+    output {
+        String tmb_txt = "${output_dir}/tmb/${name}.tmb.txt"
+    }
+}
+
 workflow call_tmb {
 
     Boolean run=true
@@ -34,27 +37,14 @@ workflow call_tmb {
     Boolean umi
 
     if (run) {
-        if (umi) {
+        call run_tmb {
-            call run_tmb as run_tmb_umi {
             input:
                 name=name,
                 file=file,
                 project=project,
-                    sample_type='c',
+                sample_type=if umi then 'c' else 't',
                 output_dir=output_dir
         }
-        }
-        if (!umi) {
-            call run_tmb as run_tmb_tissue {
-                input:
-                    name=name,
-                    file=file,
-                    project=project,
-                    sample_type='t',
-                    output_dir=output_dir
-            }
-
-        }
 
     }