linting

str/trtools/merge_str_runner.py

@@ -39,39 +39,31 @@ def main(
     # Initializing Batch
     b = get_batch()
 
-    #Initialise TRTools job to run mergeSTR
+    # Initialise TRTools job to run mergeSTR
     trtools_job = b.new_job(name='mergeSTR')
     trtools_job.image(TRTOOLS_IMAGE)
     trtools_job.cpu(8)
-    #mount using cloudfuse for reading input files 
+    # mount using cloudfuse for reading input files
     trtools_job.cloudfuse(f'cpg-{dataset}-main-analysis', '/vcffuse')
-    trtools_job.declare_resource_group(
-            vcf_output={
-                'vcf': '{root}.vcf'  
-            }
-        )
-
-    #Initialise job to zip and index the mergeSTR VCF prior to writing to output
-    zip_job = b.new_job(name = 'Zip and index')
+    trtools_job.declare_resource_group(vcf_output={'vcf': '{root}.vcf'})
+
+    # Initialise job to zip and index the mergeSTR VCF prior to writing to output
+    zip_job = b.new_job(name='Zip and index')
     zip_job.image(TRTOOLS_IMAGE)
     zip_job.cpu(8)
     zip_job.declare_resource_group(
-            vcf_output={
-                'vcf.gz':'{root}.vcf.gz',
-                'vcf.gz.tbi':'{root}.vcf.gz.tbi'
-            }
-        )
-
-
-    #read in input file paths 
+        vcf_output={'vcf.gz': '{root}.vcf.gz', 'vcf.gz.tbi': '{root}.vcf.gz.tbi'}
+    )
+
+    # read in input file paths
     vcffuse_path = []
     for id in list(internal_wgs_ids):
         vcf = os.path.join(input_dir, f'{id}_eh.reheader.vcf.gz')
         suffix = vcf.removeprefix('gs://').split('/', maxsplit=1)[1]
         vcffuse_path.append(f'/vcffuse/{suffix}')
     num_samples = len(vcffuse_path)
     vcffuse_path = ','.join(vcffuse_path)  # string format for input into mergeSTR
-    
+
     trtools_job.command(
         f"""
     mergeSTR --vcfs {vcffuse_path} --out {trtools_job.vcf_output} --vcftype eh
@@ -87,11 +79,9 @@ def main(
 
     output_path_name = output_path(f'mergeSTR_{num_samples}_samples_eh', 'analysis')
     b.write_output(zip_job.vcf_output, output_path_name)
-    
+
     b.run(wait=False)
 
+
 if __name__ == '__main__':
     main()  # pylint: disable=no-value-for-parameter
-
-
-