fix of download

ICGC-TCGA-PanCancer · Feb 15, 2018 · f542130 · f542130
1 parent 09748cc
commit f542130
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Showing 2 changed files with 4 additions and 7 deletions.
diff --git a/workflow/tools/download.py b/workflow/tools/download.py
@@ -4,13 +4,10 @@
 import os
 from utils import get_task_dict, save_output_json
 import sys
-import time
 
 task_dict = get_task_dict(sys.argv[1])
 cwd = os.getcwd()
 
-#time.sleep(2*60)
-
 def download_file(object_id, out_dir, file_name):
     docker_container = "quay.io/baminou/minibam-collab-dckr:latest"
     download_source = "collab"
@@ -27,19 +24,19 @@ def download_file(object_id, out_dir, file_name):
 # Download normal bam file
 object_id = task_dict.get('input').get('normal_bam').get('object_id')
 file_name = task_dict.get('input').get('normal_bam').get('file_name')
-#download_file(object_id, cwd, file_name)
+download_file(object_id, cwd, file_name)
 
 # Download tumor bam files
 for i in range(0,len(task_dict.get('input').get('tumor_bams'))):
     object_id = task_dict.get('input').get('tumor_bams')[i].get('object_id')
     file_name = task_dict.get('input').get('tumor_bams')[i].get('file_name')
-    #download_file(object_id, cwd, file_name)
+    download_file(object_id, cwd, file_name)
 
 # Download VCF files
 for i in range(0,len(task_dict.get('input').get('vcf_files'))):
     object_id = task_dict.get('input').get('vcf_files')[i].get('object_id')
     file_name = task_dict.get('input').get('vcf_files')[i].get('file_name')
-    #download_file(object_id, cwd, file_name)
+    download_file(object_id, cwd, file_name)
 
 save_output_json({
     'directory': cwd

diff --git a/workflow/tools/generate_minibam.py b/workflow/tools/generate_minibam.py
@@ -49,7 +49,7 @@
 with open(json_file, 'w') as f:
     json.dump(json_input, f, indent=4, sort_keys=True)
 
-#subprocess.check_output(['cwltool','--debug','--relax-path-checks','--non-strict','/home/ubuntu/pcawg-minibam/pcawg_minibam_wf.cwl',json_file])
+subprocess.check_output(['cwltool','--debug','--relax-path-checks','--non-strict','/home/ubuntu/pcawg-minibam/pcawg_minibam_wf.cwl',json_file])
 
 save_output_json({
     'output_directory': os.getcwd()