Fix tecan samplesheet for pools and python3 fixes

UMCUGenetics · Aug 9, 2021 · 70b19a8 · 70b19a8
1 parent ea091d8
commit 70b19a8
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Showing 2 changed files with 6 additions and 3 deletions.
diff --git a/clarity_epp/export/tecan.py b/clarity_epp/export/tecan.py
@@ -11,9 +11,12 @@ def samplesheet(lims, process_id, output_file):
     process = Process(lims, id=process_id)
     well_plate = {}
 
-    for placement, artifact in process.output_containers()[0].placements.iteritems():
+    for placement, artifact in process.output_containers()[0].placements.items():
         placement = ''.join(placement.split(':'))
-        well_plate[placement] = artifact.name.split('_')[0]
+        if len(artifact.samples) == 1:  # Remove 'meet_id' from artifact name if artifact is not a pool
+            well_plate[placement] = artifact.name.split('_')[0]
+        else:
+            well_plate[placement] = artifact.name
 
     for well in clarity_epp.export.utils.sort_96_well_plate(well_plate.keys()):
         output_file.write('{well}\t{sample}\n'.format(

diff --git a/clarity_epp/export/utils.py b/clarity_epp/export/utils.py
@@ -17,7 +17,7 @@ def sort_96_well_plate(wells):
     ]
     order = dict(zip(order, range(len(order))))
 
-    wells.sort(key=lambda val: order[val])
+    wells = sorted(wells, key=lambda val: order[val])
     return wells