master
parent
ab356a15f0
commit
b82438461c
|
|
@ -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 {
|
||||
# # 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: false
|
||||
#
|
||||
# # A blacklist grouping can be specified in workflow options which will inform the blacklister which workflows
|
||||
# # should share a blacklist cache.
|
||||
# groupings {
|
||||
# workflow-option: call-cache-blacklist-group
|
||||
# concurrency: 10000
|
||||
# ttl: 2 hours
|
||||
# size: 1000
|
||||
}
|
||||
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: false
|
||||
#
|
||||
# # A blacklist grouping can be specified in workflow options which will inform the blacklister which workflows
|
||||
# # should share a blacklist cache.
|
||||
# groupings {
|
||||
# workflow-option: call-cache-blacklist-group
|
||||
# concurrency: 10000
|
||||
# ttl: 2 hours
|
||||
# size: 1000
|
||||
}
|
||||
#
|
||||
# buckets {
|
||||
# # Guava cache concurrency.
|
||||
|
|
@ -201,29 +202,29 @@ google {
|
|||
# Default: just application default
|
||||
#auths = [
|
||||
|
||||
# Application default
|
||||
#{
|
||||
# name = "application-default"
|
||||
# scheme = "application_default"
|
||||
#},
|
||||
# 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 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"
|
||||
#}
|
||||
# Use service accounts provided through workflow options
|
||||
#{
|
||||
# name = "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"
|
||||
# config {
|
||||
# strict-validation: true
|
||||
# enabled: true
|
||||
# }
|
||||
# language-factory = "languages.wdl.draft3.WdlDraft3LanguageFactory"
|
||||
# config {
|
||||
# strict-validation: 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.
|
||||
# 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` 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:
|
||||
# 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
|
||||
|
|
|
|||
|
|
@ -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";
|
||||
|
|
|
|||
|
|
@ -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
|
||||
|
|
@ -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
|
||||
|
|
@ -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)
|
||||
print('#' * 50)
|
||||
print('读取日志')
|
||||
workflow_id = ''
|
||||
if match:
|
||||
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__':
|
||||
|
|
|
|||
|
|
@ -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
|
||||
}
|
||||
|
||||
|
|
|
|||
88
wdl/msi.wdl
88
wdl/msi.wdl
|
|
@ -1,29 +1,8 @@
|
|||
# msi
|
||||
|
||||
task msi_single {
|
||||
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
|
||||
task run_msi {
|
||||
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 \
|
||||
-n ${normal_rmdup_bam} \
|
||||
-t ${tumor_rmdup_bam} \
|
||||
-e ${bed} \
|
||||
-b 10 \
|
||||
-f 0.01 \
|
||||
-d /dataseq/jmdna/software/msisensor2/msi.10-50.homosite.list \
|
||||
-n ${normal_rmdup_bam} -t ${tumor_rmdup_bam} \
|
||||
-e $PUBLIC/msi/624_650_intersect_depth50_177.bed \
|
||||
-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 msi_single {
|
||||
input:
|
||||
name=tumor,
|
||||
output_dir=output_dir,
|
||||
rmdup_bam=tumor_rmdup_bam,
|
||||
bed=bed
|
||||
}
|
||||
}
|
||||
# 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
|
||||
}
|
||||
|
||||
call run_msi {
|
||||
input:
|
||||
name=tumor,
|
||||
probe=probe,
|
||||
output_dir=output_dir,
|
||||
tumor_rmdup_bam=tumor_rmdup_bam,
|
||||
normal_rmdup_bam=normal_rmdup_bam
|
||||
}
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -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 {
|
||||
|
|
|
|||
Loading…
Reference in New Issue