tumor -> tumour

ICGC-TCGA-PanCancer · Mar 12, 2018 · 4d75cc2 · 4d75cc2
1 parent 462afdd
commit 4d75cc2
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Showing 3 changed files with 8 additions and 8 deletions.
diff --git a/workflow/tools/download.py b/workflow/tools/download.py
@@ -27,9 +27,9 @@ def download_file(object_id, out_dir, 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')
+for i in range(0,len(task_dict.get('input').get('tumour_bams'))):
+    object_id = task_dict.get('input').get('tumour_bams')[i].get('object_id')
+    file_name = task_dict.get('input').get('tumour_bams')[i].get('file_name')
     download_file(object_id, cwd, file_name)
 
 # Download VCF files

diff --git a/workflow/tools/generate_minibam.py b/workflow/tools/generate_minibam.py
@@ -34,11 +34,11 @@
 json_input['indel-padding']                     = str(task_dict.get('input').get('indel_padding'))
 
 json_input['tumours'] = []
-for i in range(0,len(task_dict.get('input').get('tumor_bams'))):
+for i in range(0,len(task_dict.get('input').get('tumour_bams'))):
     tmp_json = {}
-    tmp_json['tumourId'] = task_dict.get('input').get('tumor_bams')[i].get('file_name').replace('.bam','')
-    tmp_json['bamFileName'] = task_dict.get('input').get('tumor_bams')[i].get('file_name')
-    tmp_json['oxoQScore'] = task_dict.get('input').get('tumor_bams')[i].get('oxog_score')
+    tmp_json['tumourId'] = task_dict.get('input').get('tumour_bams')[i].get('file_name').replace('.bam','')
+    tmp_json['bamFileName'] = task_dict.get('input').get('tumour_bams')[i].get('file_name')
+    tmp_json['oxoQScore'] = task_dict.get('input').get('tumour_bams')[i].get('oxog_score')
     tmp_json['associatedVcfs'] = []
     for j in range(0,len(task_dict.get('input').get('vcf_files'))):
         tmp_json['associatedVcfs'].append(task_dict.get('input').get('vcf_files')[j].get('file_name'))

diff --git a/workflow/tools/generate_song_payloads.py b/workflow/tools/generate_song_payloads.py
@@ -18,7 +18,7 @@
 
 input_directory = task_dict.get('input').get('input_directory')
 normal_bam = task_dict.get('input').get('normal_bam')
-tumor_bams = task_dict.get('input').get('tumor_bams')
+tumor_bams = task_dict.get('input').get('tumour_bams')
 experiment = task_dict.get('input').get('experiment')
 indel_padding = task_dict.get('input').get('indel_padding')
 snv_padding = task_dict.get('input').get('snv_padding')