Apply suggestions from code review

Co-authored-by: April Shen <[email protected]>
EBIvariation · Aug 30, 2024 · f76b155 · f76b155
1 parent 06e3b23
commit f76b155
Show file tree

Hide file tree

Showing 2 changed files with 2 additions and 2 deletions.
diff --git a/eva_sub_cli/nextflow/validation.nf b/eva_sub_cli/nextflow/validation.nf
@@ -237,7 +237,7 @@ process sample_name_concordance {
 
     script:
     """
-    $params.python_scripts.samples_checker --metadata_json $metadata_json --vcf_files $vcf_files --output_yaml sample_checker.yml > sample_checker.log
+    $params.python_scripts.samples_checker --metadata_json $metadata_json --vcf_files $vcf_files --output_yaml sample_checker.yml > sample_checker.log 2>&1
     """
 }
 

diff --git a/eva_sub_cli/submit.py b/eva_sub_cli/submit.py
@@ -65,7 +65,7 @@ def _upload_file(self, submission_upload_url, input_file):
         base_name = os.path.basename(input_file)
         self.debug(f'Transfer {base_name} to EVA FTP')
         with open(input_file, 'rb') as f:
-            r = requests.put(os.path.join(submission_upload_url, base_name), data=open(input_file, 'rb'))
+            r = requests.put(os.path.join(submission_upload_url, base_name), data=f)
         r.raise_for_status()
         self.debug(f'Upload of {base_name} completed')