Merge branch '34-CheckcheckDesign' into 'develop'

Fix #34 to remove trailing and leading whitespace in design file contents

Closes #34

See merge request !54

CHANGELOG.md

@@ -3,7 +3,7 @@
 * Change Cellranger Version to 3.1.0
 * Fix countDesign to take multiple samples
 * Add MIT License
-* Check Design File for spaces in name
+* Check Design File for spaces in name and file contents
 * Update design example, README, and astrocyte.yml with current barcode IDs
 
 **Background**

workflow/scripts/check_design.py

@@ -55,7 +55,7 @@ def check_design_headers(design):
     if len(missing_headers) > 0:
         logger.error('Missing column headers: %s', list(missing_headers))
         raise Exception("Missing column headers: %s" % list(missing_headers))
-    
+
     return design
 
 def main():
@@ -67,7 +67,7 @@ def main():
     logger.addHandler(handler)
 
     # Read files as dataframes
-    design_df = pd.read_csv(args.design, sep=',')
+    design_df = pd.read_csv(args.design, sep=',', converters={'Lane': str.strip, 'Sample': str.strip, 'Index': str.strip})
 
     # Check design file
     new_design_df = check_design_headers(design_df)
@@ -75,4 +75,4 @@ def main():
     new_design_df.to_csv('design.checked.csv', header=True, sep=',', index=False)
 
 if __name__ == '__main__':
-    main()
\ No newline at end of file
+    main()