更新

codes/cromwell.examples.conf

@@ -56,6 +56,7 @@ system {
   # Default number of cache read workers
   number-of-cache-read-workers = 25
 
+
   io {
     # throttle {
     # # Global Throttling - This is mostly useful for GCS and can be adjusted to match
@@ -158,19 +159,19 @@ call-caching {
   # 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
+    #   # 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.
+    #   # hit ids or buckets of cache hit paths that Cromwell has previously failed to copy for permissions reasons.
-     enabled: false
+    enabled: false
-  #
+    #
-  #   # A blacklist grouping can be specified in workflow options which will inform the blacklister which workflows
+    #   # A blacklist grouping can be specified in workflow options which will inform the blacklister which workflows
-  #   # should share a blacklist cache.
+    #   # should share a blacklist cache.
-  #   groupings {
+    #   groupings {
-  #     workflow-option: call-cache-blacklist-group
+    #     workflow-option: call-cache-blacklist-group
-  #     concurrency: 10000
+    #     concurrency: 10000
-  #     ttl: 2 hours
+    #     ttl: 2 hours
-  #     size: 1000
+    #     size: 1000
-     }
+  }
   #
   #   buckets {
   #     # Guava cache concurrency.
@@ -201,29 +202,29 @@ google {
   # Default: just application default
   #auths = [
 
-    # Application default
+  # Application default
-    #{
+  #{
-    #  name = "application-default"
+  #  name = "application-default"
-    #  scheme = "application_default"
+  #  scheme = "application_default"
-    #},
+  #},
 
-    # Use a static service account
+  # Use a static service account
-    #{
+  #{
-    #  name = "service-account"
+  #  name = "service-account"
-    #  scheme = "service_account"
+  #  scheme = "service_account"
-    #  Choose between PEM file and JSON file as a credential format. They're mutually exclusive.
+  #  Choose between PEM file and JSON file as a credential format. They're mutually exclusive.
-    #  PEM format:
+  #  PEM format:
-    #  service-account-id = "my-service-account"
+  #  service-account-id = "my-service-account"
-    #  pem-file = "/path/to/file.pem"
+  #  pem-file = "/path/to/file.pem"
-    #  JSON format:
+  #  JSON format:
-    #  json-file = "/path/to/file.json"
+  #  json-file = "/path/to/file.json"
-    #}
+  #}
 
-    # Use service accounts provided through workflow options
+  # Use service accounts provided through workflow options
-    #{
+  #{
-    #   name = "user-service-account"
+  #   name = "user-service-account"
-    #   scheme = "user_service_account"
+  #   scheme = "user_service_account"
-    #}
+  #}
   #]
 }
 
@@ -292,11 +293,11 @@ languages {
       }
       # draft-3 is the same as 1.0 so files should be able to be submitted to Cromwell as 1.0
       # "draft-3" {
-        # language-factory = "languages.wdl.draft3.WdlDraft3LanguageFactory"
+      # language-factory = "languages.wdl.draft3.WdlDraft3LanguageFactory"
-        # config {
+      # config {
-        #   strict-validation: true
+      #   strict-validation: true
-        #   enabled: true
+      #   enabled: true
-        # }
+      # }
       # }
       "1.0" {
         # 1.0 is just a rename of draft-3, so yes, they really do use the same factory:
@@ -378,11 +379,11 @@ backend {
         # To turn off the default `sync` behavior set this value to an empty string:
         # script-epilogue = ""
 
-	# `glob-link-command` specifies command used to link glob outputs, by default using hard-links.
+        # `glob-link-command` specifies command used to link glob outputs, by default using hard-links.
-	# If filesystem doesn't allow hard-links (e.g., beeGFS), change to soft-links as follows:
+        # If filesystem doesn't allow hard-links (e.g., beeGFS), change to soft-links as follows:
-	# glob-link-command = "ln -sL GLOB_PATTERN GLOB_DIRECTORY"
+        # glob-link-command = "ln -sL GLOB_PATTERN GLOB_DIRECTORY"
 
-	# The list of possible runtime custom attributes.
+        # The list of possible runtime custom attributes.
         runtime-attributes = """
         String? docker
         String? docker_user

codes/filter_snpindel.pl

@@ -8,11 +8,11 @@ die "useage:perl $0 input out tag_out project sample_type pipeline" unless @ARGV
 my ($input, $out, $tag_out, $project, $sample_type, $pipeline) = @ARGV;
 
 my $public_path = defined $ENV{'PUBLIC'} ? $ENV{'PUBLIC'} : "/dataseq/jmdna/codes/public";
-print "SnpIndel过滤使用public路径：$public_path\n";
+print "$pipeline 过滤使用public路径：$public_path\n";
 
 my $database_path = defined $ENV{'DATABASE'} ? $ENV{'DATABASE'} : "/dataseq/jmdna/codes/reportbase";
 
-print "SnpIndel过滤使用database路径：$database_path\n";
+print "$pipeline 过滤使用database路径：$database_path\n";
 
 # open OUT, ">$**.hg19_multianno_filter.txt";
 open OUT, "> $out";

codes/public/msi/624_650_160_intersect_74.bed

@@ -0,0 +1,74 @@
+chr1	161293492	161293503
+chr1	161309335	161309346
+chr1	161332091	161332105
+chr1	204495595	204495609
+chr2	29449344	29449368
+chr2	47600581	47600591
+chr2	47635523	47635536
+chr2	47641559	47641586
+chr2	47702451	47702470
+chr2	48032740	48032753
+chr2	48033890	48033908
+chr2	58390218	58390230
+chr2	58453843	58453855
+chr2	209101905	209101915
+chr2	212495336	212495347
+chr2	212578379	212578393
+chr2	215657182	215657198
+chr3	37067099	37067120
+chr3	142231062	142231080
+chr3	142241692	142241704
+chr3	142259706	142259720
+chr3	142274739	142274749
+chr4	25666785	25666805
+chr4	55598211	55598236
+chr4	55976947	55976960
+chr4	153268227	153268241
+chr5	112111309	112111322
+chr5	131924363	131924373
+chr5	131927550	131927560
+chr6	32790099	32790109
+chr6	117642992	117643012
+chr7	6037057	6037074
+chr7	116409675	116409690
+chr7	140434574	140434585
+chr7	140434586	140434596
+chr9	5073681	5073691
+chr9	80343587	80343601
+chr9	135773000	135773018
+chr10	8115668	8115686
+chr10	43595836	43595850
+chr10	89720633	89720648
+chr11	108114661	108114676
+chr11	108119615	108119629
+chr11	108121410	108121425
+chr11	108141955	108141970
+chr11	108151697	108151707
+chr11	108188266	108188279
+chr12	69214081	69214093
+chr12	133237753	133237767
+chr13	28609813	28609823
+chr13	32893197	32893207
+chr13	32907535	32907546
+chr13	48954159	48954172
+chr13	48954282	48954293
+chr13	48955363	48955373
+chr13	49039094	49039118
+chr14	68944343	68944357
+chr14	69006883	69006908
+chr14	69149592	69149604
+chr14	69149627	69149647
+chr17	7572154	7572172
+chr17	7578711	7578729
+chr17	29482977	29482987
+chr17	29508819	29508835
+chr17	29528406	29528416
+chr17	29559061	29559087
+chr17	29663614	29663625
+chr17	29663625	29663636
+chr17	37855713	37855727
+chr17	59857599	59857610
+chr20	43962585	43962595
+chr20	43962640	43962652
+chr20	43963436	43963446
+chr19	50911947	50911959

codes/public/msi/624_650_intersect_depth50_177.bed

@@ -0,0 +1,177 @@
+chr1	16200729	16200739
+chr1	16248728	16248739
+chr1	78414310	78414328
+chr1	78432647	78432658
+chr1	78432658	78432668
+chr1	78435701	78435713
+chr1	161293492	161293503
+chr1	161309335	161309346
+chr1	161332091	161332105
+chr1	204495595	204495609
+chr1	243736210	243736225
+chr2	29449344	29449368
+chr2	39536689	39536716
+chr2	47600581	47600591
+chr2	47635523	47635536
+chr2	47641559	47641586
+chr2	47702451	47702470
+chr2	48032740	48032753
+chr2	48033890	48033908
+chr2	58390218	58390230
+chr2	58453843	58453855
+chr2	61143993	61144003
+chr2	61145498	61145511
+chr2	61726050	61726061
+chr2	95849361	95849384
+chr2	136873827	136873837
+chr2	141625834	141625853
+chr2	173435578	173435592
+chr2	190717517	190717527
+chr2	198257673	198257683
+chr2	198267243	198267256
+chr2	209101905	209101915
+chr2	212495336	212495347
+chr2	212578379	212578393
+chr2	215657182	215657198
+chr2	225422600	225422622
+chr3	30691871	30691881
+chr3	47103861	47103875
+chr3	52696310	52696321
+chr3	69988437	69988451
+chr3	89448876	89448888
+chr3	138400782	138400795
+chr3	142231062	142231080
+chr3	142241692	142241704
+chr3	142259706	142259720
+chr3	142274739	142274749
+chr3	156413615	156413632
+chr3	169988364	169988384
+chr3	169992975	169992993
+chr3	185009691	185009711
+chr3	185010850	185010860
+chr3	185080912	185080922
+chr3	185155430	185155441
+chr3	191888452	191888465
+chr4	1919852	1919862
+chr4	25666785	25666805
+chr4	55135777	55135789
+chr4	55135811	55135827
+chr4	55598211	55598236
+chr4	55976947	55976960
+chr4	106162144	106162154
+chr4	142950186	142950196
+chr4	153268227	153268241
+chr4	185340725	185340745
+chr5	38959431	38959441
+chr5	38978758	38978769
+chr5	67576330	67576345
+chr5	67584512	67584524
+chr5	112111309	112111322
+chr5	131924363	131924373
+chr5	131927550	131927560
+chr5	170818290	170818300
+chr5	170837513	170837526
+chr6	32790099	32790109
+chr6	106534484	106534496
+chr6	117642992	117643012
+chr6	134494708	134494721
+chr6	138192324	138192335
+chr6	162683814	162683835
+chr6	163899794	163899806
+chr6	163991476	163991492
+chr6	163991598	163991608
+chr7	6037057	6037074
+chr7	116409675	116409690
+chr7	116414203	116414214
+chr7	140421095	140421107
+chr7	140425499	140425511
+chr7	140482263	140482279
+chr7	140484450	140484462
+chr7	140487100	140487124
+chr7	140489019	140489029
+chr7	140496148	140496164
+chr7	140498359	140498380
+chr7	148543693	148543704
+chrX	39930433	39930446
+chrX	44920541	44920551
+chrX	44935924	44935937
+chrX	44949951	44949962
+chrX	123184949	123184968
+chrX	123204978	123204992
+chr8	38138963	38138974
+chr8	38175279	38175290
+chr8	38316067	38316077
+chr8	38321488	38321499
+chr8	38321830	38321853
+chr8	117864952	117864966
+chr8	117868531	117868554
+chr8	141754888	141754904
+chr9	5073681	5073691
+chr9	80343587	80343601
+chr9	87357642	87357652
+chr9	87430433	87430449
+chr9	87487518	87487529
+chr9	135773000	135773018
+chr10	8115668	8115686
+chr10	43595836	43595850
+chr10	89720633	89720648
+chr11	94212930	94212941
+chr11	102193508	102193534
+chr11	108114661	108114676
+chr11	108119615	108119629
+chr11	108121410	108121425
+chr11	108141955	108141970
+chr11	108151697	108151707
+chr11	108188266	108188279
+chr11	118369265	118369280
+chr11	119144791	119144808
+chr11	125490765	125490786
+chr12	463405	463415
+chr12	69214081	69214093
+chr12	112893675	112893692
+chr12	133237753	133237767
+chr13	26959325	26959335
+chr13	26967477	26967488
+chr13	28961945	28961960
+chr13	28962591	28962602
+chr13	28963283	28963296
+chr13	28980036	28980046
+chr13	32893197	32893207
+chr13	32907535	32907546
+chr13	48954159	48954172
+chr13	48954282	48954293
+chr13	48955363	48955373
+chr13	49039094	49039118
+chr14	23652346	23652367
+chr14	68944343	68944357
+chr14	68964202	68964214
+chr14	69006883	69006908
+chr14	69149592	69149604
+chr14	69149627	69149647
+chr15	99439963	99439973
+chr16	3808052	3808065
+chr16	9934670	9934690
+chr17	7572154	7572172
+chr17	7577678	7577694
+chr17	7578711	7578729
+chr17	29482977	29482987
+chr17	29508819	29508835
+chr17	29528406	29528416
+chr17	29559061	29559087
+chr17	29663614	29663625
+chr17	29663625	29663636
+chr17	37855713	37855727
+chr17	47696764	47696774
+chr17	59857599	59857610
+chr17	66526937	66526947
+chr17	66527166	66527177
+chr18	60969534	60969548
+chr20	43962585	43962595
+chr20	43962640	43962652
+chr20	43963436	43963446
+chr20	52188399	52188409
+chr19	1225275	1225288
+chr19	1228058	1228069
+chr19	50911947	50911959
+chr22	41545024	41545038
+chr22	41550984	41550995

codes/run_wdl.py

@@ -3,6 +3,7 @@
 import argparse
 import json
 import os
+import re
 import subprocess
 import time
 from datetime import datetime
@@ -98,7 +99,6 @@ def run(barcode, normal, umi, input_dir, output_dir, project, cancer, probe, wdl
 
     # 记录开始时间
     start_time = time.time()
-    print(cmd)
     ret = subprocess.Popen(cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE, encoding="utf-8")
     pidnum = ret.pid
     with open(os.path.join(output_dir, 'pid'), 'w') as pidfile:
@@ -106,16 +106,61 @@ def run(barcode, normal, umi, input_dir, output_dir, project, cancer, probe, wdl
     # ret.wait()
     # 等待进程完成，并获取输出和错误
     output, error = ret.communicate()
+    print(output, error)
+
+    stdout = open(os.path.join(output_dir, f'{args.barcode}_{logname}_stdout.log'), 'w')
+    stderr = open(os.path.join(output_dir, f'{args.barcode}_{logname}_stderr.log'), 'w')
+
     # 记录结束时间
     end_time = time.time()
     # 计算运行时间
     elapsed_time = end_time - start_time
 
-    print("\n运行时间：{:.2f} 秒".format(elapsed_time))
+    # 使用正则表达式提取UUID
+    match = re.search(r'UUID\(([^)]+)\)', output, re.MULTILINE)
 
-    print(output, error)
+    workflow_id = ''
-    print('#' * 50)
+    if match:
-    print('读取日志')
+        workflow_id = match.group(1)
+        stdout.write(f"任务 ID: {workflow_id}\n\n")
+    else:
+        stderr.write("未提取到任务 ID\n\n")
+
+    stdout.write("任务耗时: {:.2f} 秒\n\n".format(elapsed_time))
+
+    workflow_path = os.path.join(output_dir, 'cromwell-executions', 'pipeline', workflow_id)
+    stdout.write(f'workflow 地址: {workflow_path}\n\n')
+
+    stdout_files = list()
+    stderr_files = list()
+    for root, dirs, files in os.walk(workflow_path):
+        for file in files:
+            if str(file).endswith('stdout'):
+                file_path = os.path.join(root, file)
+                stdout_files.append(str(file_path))
+            if str(file).endswith('stderr'):
+                file_path = os.path.join(root, file)
+                stderr_files.append(str(file_path))
+
+    # 按照文件的修改时间倒序排序
+    sorted_stdout_files = sorted(stdout_files, key=lambda x: os.path.getmtime(x), reverse=True)
+    sorted_stderr_files = sorted(stderr_files, key=lambda x: os.path.getmtime(x), reverse=True)
+
+    for file_path in sorted_stdout_files:
+        with open(file_path, 'r') as f:
+            stdout.write('#' * 50 + '\n')
+            stdout.write(file_path + '\n')
+            stdout.write(f.read())
+            stdout.write('\n\n')
+
+    for file_path in sorted_stderr_files:
+        with open(file_path, 'r') as f:
+            stderr.write('#' * 50 + '\n')
+            stderr.write(file_path + '\n')
+            stderr.write(f.read())
+            stderr.write('\n\n')
+    stdout.close()
+    stderr.close()
 
 
 if __name__ == '__main__':

pipeline.wdl

@@ -140,9 +140,8 @@ workflow pipeline {
             run=catecode['addMsi'],
             tumor=tumor,
             tumor_rmdup_bam=alignment.tumor_rmdup_bam,
-            normal=normal,
             normal_rmdup_bam=alignment.normal_rmdup_bam,
-            bed=bed,
+            probe=probe,
             output_dir=workdir
     }
 

wdl/msi.wdl

@@ -1,29 +1,8 @@
 # msi
 
-task msi_single {
+task run_msi {
-    String name
-    String bed
-    String output_dir
-    String rmdup_bam
-
-    command <<<
-        if [ ! -d ${output_dir}/msi ];then
-        mkdir ${output_dir}/msi
-        fi
-
-        msisensor2 msi \
-        -M /dataseq/jmdna/software/msisensor2/models_hg19_GRCh37 \
-        -t ${output_dir}/alignment/${name}.rmdup.bam \
-        -e ${bed} \
-        -b 10 \
-        -o ${output_dir}/msi/${name}.msi.txt
-    >>>
-
-}
-
-task msi_paired {
-    String bed
     String name
+    String probe
     String output_dir
     String tumor_rmdup_bam
     String normal_rmdup_bam
@@ -33,14 +12,36 @@ task msi_paired {
         mkdir ${output_dir}/msi
         fi
 
+        if [ "${probe}" == "682" ]; then
+
+        echo "msi 682探针 "
         msisensor2 msi \
-        -d /dataseq/jmdna/software/msisensor2/hg19.microsatellites.list \
+        -f 0.01 \
-        -n ${normal_rmdup_bam} \
+        -d /dataseq/jmdna/software/msisensor2/msi.10-50.homosite.list \
-        -t ${tumor_rmdup_bam} \
+        -n ${normal_rmdup_bam} -t ${tumor_rmdup_bam} \
-        -e ${bed} \
+        -e $PUBLIC/msi/624_650_intersect_depth50_177.bed \
-        -b 10 \
+        -b 10 -c 30 -o ${output_dir}/msi/${name}.msi.txt
+
+        elif [ "${probe}" == "624" ]; then
+
+        echo "msi 624 探针 "
+        msisensor2 msi \
+        -M /dataseq/jmdna/software/msisensor2/models_hg19_GRCh37 \
+        -t ${tumor_rmdup_bam} -e $PUBLIC/msi//624_650_intersect_depth50_177.bed -b 10 \
         -o ${output_dir}/msi/${name}.msi.txt
 
+        elif [ "${probe}" == "160" ]; then
+
+        echo "msi 624 探针 "
+        msisensor2 msi \
+        -M /dataseq/jmdna/software/msisensor2/models_hg19_GRCh37 \
+        -t -e $PUBLIC/msi/624_650_160_intersect_74.bed \
+        -b 10 ${output_dir}/msi/${name}.msi.txt
+
+        else
+        echo "未知的选项: ${probe}"
+        fi
+
     >>>
 
 }
@@ -48,34 +49,21 @@ task msi_paired {
 workflow call_msi {
     Boolean run=true
 
+    String probe
     String tumor
     String tumor_rmdup_bam
-    String? normal
     String? normal_rmdup_bam
-    String bed
     String output_dir
 
     if (run) {
-        # 单样本
+
-        if (!defined(normal)) {
+        call run_msi {
-            call msi_single {
+            input:
-                input:
+                name=tumor,
-                    name=tumor,
+                probe=probe,
-                    output_dir=output_dir,
+                output_dir=output_dir,
-                    rmdup_bam=tumor_rmdup_bam,
+                tumor_rmdup_bam=tumor_rmdup_bam,
-                    bed=bed
+                normal_rmdup_bam=normal_rmdup_bam
-            }
-        }
-        # 双样本
-        if (defined(normal)) {
-            call msi_paired {
-                input:
-                    name=tumor,
-                    bed=bed,
-                    output_dir=output_dir,
-                    tumor_rmdup_bam=tumor_rmdup_bam,
-                    normal_rmdup_bam=normal_rmdup_bam
-            }
         }
     }
 

wdl/postprocess.wdl

@@ -23,7 +23,6 @@ task run_post {
         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 {