sample_id_column

Author: antgonza

src/sequence_processing_pipeline/NuQCJob.py

@@ -379,8 +379,15 @@ def _process_sample_sheet(self):
             raise PipelineError(s)
 
         sample_ids = []
+        # long_reads use the Sample_Name as the main sample identifier,
+        # everything else uses Sample_ID; we might want to change this
+        # in the future for everything to use Sample_Name
+        sample_id_column = 'Sample_ID'
+        if self.read_length == 'long':
+            sample_id_column = 'Sample_Name'
         for sample in sheet.samples:
-            sample_ids.append((sample['Sample_ID'], sample['Sample_Project']))
+            sample_ids.append(
+                (sample[sample_id_column], sample['Sample_Project']))
 
         bioinformatics = sheet.Bioinformatics