tumor -> tumour

workflow/main.yaml

@@ -78,7 +78,7 @@ workflow:
                   type: string
                 specimen_type:
                   type: string
-    tumor_bams:
+    tumour_bams:
       type: array
       items:
         type: object
@@ -146,7 +146,7 @@ workflow:
       tool: download_files
       input:
         normal_bam: normal_bam
-        tumor_bams: tumor_bams
+        tumour_bams: tumour_bams
         vcf_files: associated_vcfs
       depends_on: null
 
@@ -155,7 +155,7 @@ workflow:
       input:
         input_directory: directory@download_files
         normal_bam: normal_bam
-        tumor_bams: tumor_bams
+        tumour_bams: tumour_bams
         vcf_files: associated_vcfs
         sv_padding: sv_padding
         snv_padding: snv_padding
@@ -169,7 +169,7 @@ workflow:
       input:
         input_directory: directory@download_files
         normal_bam: normal_bam
-        tumor_bams: tumor_bams
+        tumour_bams: tumour_bams
         experiment: experiment
         indel_padding: indel_padding
         snv_padding: snv_padding
@@ -209,7 +209,7 @@ tools:
     input:
       normal_bam:
         type: object
-      tumor_bams:
+      tumour_bams:
         type: array
       vcf_files:
         type: array
@@ -224,7 +224,7 @@ tools:
         type: string
       normal_bam:
         type: object
-      tumor_bams:
+      tumour_bams:
         type: array
       vcf_files:
         type: array
@@ -245,7 +245,7 @@ tools:
         type: string
       normal_bam:
         type: object
-      tumor_bams:
+      tumour_bams:
         type: array
       experiment:
         type: object

workflow/tools/download.py

@@ -26,7 +26,7 @@ def download_file(object_id, out_dir, file_name):
 file_name = task_dict.get('input').get('normal_bam').get('file_name')
 download_file(object_id, cwd, file_name)
 
-# Download tumor bam files
+# Download tumour bam files
 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')

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('tumour_bams')
+tumour_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')
@@ -73,9 +73,9 @@ def create_payload_json(bam, experiment, input_directory, output_file, associate
 create_payload_json(normal_bam, experiment, input_directory, os.path.join(input_directory, 'normal_minibam.json'), associated_vcfs)
 payloads.append('normal_minibam.json')
 
-for i in range(0,len(tumor_bams)):
-    create_payload_json(tumor_bams[i], experiment, input_directory, os.path.join(input_directory, 'tumor_minibam_'+str(i)+'.json'), associated_vcfs)
-    payloads.append( 'tumor_minibam_'+str(i)+'.json')
+for i in range(0,len(tumour_bams)):
+    create_payload_json(tumour_bams[i], experiment, input_directory, os.path.join(input_directory, 'tumour_minibam_'+str(i)+'.json'), associated_vcfs)
+    payloads.append( 'tumour_minibam_'+str(i)+'.json')
 
 save_output_json({
     'payloads': payloads