Merge pull request #36 from UMCUGenetics/hotfix/v1.5.1

Hotfix - v1.5.1
UMCUGenetics · Jan 25, 2022 · 2539225 · 2539225
2 parents 4744c39 + dd6aef4
commit 2539225
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Showing 4 changed files with 26 additions and 13 deletions.
diff --git a/clarity_epp/export/caliper.py b/clarity_epp/export/caliper.py
@@ -1,4 +1,5 @@
 """Caliper export functions."""
+import string
 
 from genologics.entities import Process
 
@@ -187,6 +188,15 @@ def samplesheet_dilute(lims, process_id, output_file):
             volume_water=ul_water
         )
 
-    # Write output, sort by well
-    for well in clarity_epp.export.utils.sort_96_well_plate(output.keys()):
-        output_file.write(output[well])
+    wells = []
+    for col in range(1, 13):
+        wells.extend(['{}{}'.format(row, str(col)) for row in string.ascii_uppercase[:8]])
+
+    for well in wells:
+        if well in output:
+            output_file.write(output[well])
+        else:
+            output_file.write('Leeg\tNone\t{well}\t{plate_id_output}\t0\t0\n'.format(
+                well=well,
+                plate_id_output=output_artifact.location[0].name,
+            ))
diff --git a/clarity_epp/export/magnis.py b/clarity_epp/export/magnis.py
@@ -15,11 +15,11 @@ def samplesheet(lims, process_id, output_file):
         well_strip[placement] = artifact.name
 
     # Write Header
-    output_file.write('sample_id\tinstrument_name\n')
+    output_file.write('sampleInstrument\n')
 
     # Write samples
     for well in clarity_epp.export.utils.sort_96_well_plate(well_strip.keys()):
-        output_file.write('{sample}\t{instrument_name}\n'.format(
+        output_file.write('{sample}{instrument_name}\n'.format(
             sample=well_strip[well],
-            instrument_name=process.udf['Instrument naam']
+            instrument_name=process.udf['Instrument naam'].capitalize()
         ))
diff --git a/clarity_epp/export/sample.py b/clarity_epp/export/sample.py
@@ -145,7 +145,10 @@ def sample_indications(lims, output_file, artifact_name=None, sequencing_run=Non
         output_file.write('Sample\tIndication\n')
         for sample_name, sample in samples.items():
             output_file.write(
-                '{sample}\t{indication}\n'.format(sample=sample_name, indication=sample.udf['Dx Onderzoeksindicatie'])
+                '{sample}\t{indication}\n'.format(
+                    sample=sample_name,
+                    indication=sample.udf['Dx Onderzoeksindicatie'].split(';')[0]  # select newest indication
+                )
             )
     else:
-        print("Can't find sample(s).")
+        print("no_sample_found")
diff --git a/clarity_epp/qc/illumina.py b/clarity_epp/qc/illumina.py
@@ -7,11 +7,11 @@ def set_avg_q30(lims, process_id):
     process = Process(lims, id=process_id)
     artifact = process.analytes()[0][0]
 
-    if all([udf in artifact.udf for udf in ['% Bases >=Q30 R1', 'Yield PF (Gb) R1', '% Bases >=Q30 R2', 'Yield PF (Gb) R2']]):
-        r1_q30 = artifact.udf['% Bases >=Q30 R1']
-        r1_yield = artifact.udf['Yield PF (Gb) R1']
-        r2_q30 = artifact.udf['% Bases >=Q30 R2']
-        r2_yield = artifact.udf['Yield PF (Gb) R2']
+    if all([udf in artifact.container.udf for udf in ['% Bases >=Q30 R1', 'Yield PF (Gb) R1', '% Bases >=Q30 R2', 'Yield PF (Gb) R2']]):
+        r1_q30 = artifact.container.udf['% Bases >=Q30 R1']
+        r1_yield = artifact.container.udf['Yield PF (Gb) R1']
+        r2_q30 = artifact.container.udf['% Bases >=Q30 R2']
+        r2_yield = artifact.container.udf['Yield PF (Gb) R2']
 
         average_q30 = (r1_q30*r1_yield + r2_q30*r2_yield) / (r1_yield+r2_yield)