Merge pull request #12 from OpenOmics/sample_name_parsing

Sample name parsing

Author: chenv3

src/run.py

@@ -506,15 +506,15 @@ def add_sample_metadata(input_files, config, group=None):
     for file in input_files:
         # Split sample name on file extension
         sample = re.split(r"(_S[0-9]+)(_L[0-9]{3})?\.R[12]\.f(ast)?q.gz", os.path.basename(file))[0]
+        if os.path.basename(file) == sample:
+            # Sample has a non-standard name, print warning message
+            err("Warning: Sample '{0}' has a file name that is not compatible with cellranger! Skipping over input file...".format(os.path.basename(file)))
+            continue
         if sample not in added:
             # Only add PE sample information once
             added.append(sample)
             config['samples'].append(sample)
-        if os.path.basename(file) == sample:
-            # Sample has a non-standard name,
-            # print warning message
-            err("Warning: Sample '{0}' has a file name that is not compatible with cellranger! Skipping over input file...".format(os.path.basename(file)))
-            continue
+
     return config