From ce04443a00b5e245fb3799067b1355ef6f22d946 Mon Sep 17 00:00:00 2001
From: Robert Ernst <r.f.ernst-3@umcutrecht.nl>
Date: Tue, 13 Sep 2022 13:10:25 +0200
Subject: [PATCH 01/41] Remove, reviewer answer, unavailable while running

---
 clarity_epp/export/email.py | 13 +++++++++----
 1 file changed, 9 insertions(+), 4 deletions(-)

diff --git a/clarity_epp/export/email.py b/clarity_epp/export/email.py
index addf6c1..c27a9bc 100644
--- a/clarity_epp/export/email.py
+++ b/clarity_epp/export/email.py
@@ -22,7 +22,12 @@ def sequencing_run(lims, email_settings, process_id):
 
     if process.step.actions.escalation:
         message += "\nManager Review LIMS:\n"
-        message += "{0}: {1}\n".format(process.step.actions.escalation['author'].name, process.step.actions.escalation['request'])
-        message += "{0}: {1}\n".format(process.step.actions.escalation['reviewer'].name, process.step.actions.escalation['answer'])
-
-    send_email(email_settings['server'], email_settings['from'], email_settings['to_sequencing_run_complete'], subject, message)
+        message += "{0}: {1}\n".format(
+            process.step.actions.escalation['author'].name,
+            process.step.actions.escalation['request']
+        )
+
+    send_email(
+        email_settings['server'], email_settings['from'], email_settings['to_sequencing_run_complete'],
+        subject, message
+    )

From 6b6f0f0f3e7f1cdca74f310f554c6557be2ac552 Mon Sep 17 00:00:00 2001
From: Robert Ernst <r.f.ernst-3@umcutrecht.nl>
Date: Wed, 12 Oct 2022 11:06:36 +0200
Subject: [PATCH 02/41] Add tecan purify_normalise samplesheet

---
 clarity_epp/export/tecan.py | 23 ++++++++++++++++-------
 1 file changed, 16 insertions(+), 7 deletions(-)

diff --git a/clarity_epp/export/tecan.py b/clarity_epp/export/tecan.py
index e444c23..a47ab2f 100755
--- a/clarity_epp/export/tecan.py
+++ b/clarity_epp/export/tecan.py
@@ -5,9 +5,8 @@
 import clarity_epp.export.utils
 
 
-def samplesheet(lims, process_id, output_file):
+def samplesheet_qc(lims, process_id, type, output_file):
     """Create Tecan samplesheet."""
-    output_file.write('Position\tSample\n')
     process = Process(lims, id=process_id)
     well_plate = {}
 
@@ -18,8 +17,18 @@ def samplesheet(lims, process_id, output_file):
         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(
-            well=well,
-            sample=well_plate[well]
-        ))
+    if type == 'qc':
+        output_file.write('Position\tSample\n')
+        for well in clarity_epp.export.utils.sort_96_well_plate(well_plate.keys()):
+            output_file.write('{well}\t{sample}\n'.format(
+                well=well,
+                sample=well_plate[well]
+            ))
+
+    elif type == 'purify_normalise':
+        output_file.write('Sample\tPosition\n')
+        for well in clarity_epp.export.utils.sort_96_well_plate(well_plate.keys()):
+            output_file.write('{sample}\t{well}\n'.format(
+                sample=well_plate[well],
+                well=well
+            ))
\ No newline at end of file

From 64d4cbc9a16001b6126b8b9034b093eb69147eb7 Mon Sep 17 00:00:00 2001
From: Robert Ernst <r.f.ernst-3@umcutrecht.nl>
Date: Wed, 12 Oct 2022 11:07:06 +0200
Subject: [PATCH 03/41] Add tecan purify_normalise samplesheet

---
 clarity_epp.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/clarity_epp.py b/clarity_epp.py
index 86eb90d..2c69795 100755
--- a/clarity_epp.py
+++ b/clarity_epp.py
@@ -128,7 +128,7 @@ def export_tapestation(args):
 
 def export_tecan(args):
     """Export samplesheets for tecan machine."""
-    clarity_epp.export.tecan.samplesheet(lims, args.process_id, args.output_file)
+    clarity_epp.export.tecan.samplesheet(lims, args.process_id, args.type, args.output_file)
 
 
 def export_workflow(args):
@@ -330,6 +330,7 @@ def placement_complete_step(args):
 
     parser_export_tecan = subparser_export.add_parser('tecan', help='Create tecan samplesheets', parents=[output_parser])
     parser_export_tecan.add_argument('process_id', help='Clarity lims process id')
+    parser_export_tecan.add_argument('type', choices=['qc', 'purify_normalise'], help='Samplesheet type')
     parser_export_tecan.set_defaults(func=export_tecan)
 
     parser_export_workflow = subparser_export.add_parser(

From 4f26923342568eda7d9766f785af1f4e71cb72c8 Mon Sep 17 00:00:00 2001
From: Robert Ernst <r.f.ernst-3@umcutrecht.nl>
Date: Wed, 12 Oct 2022 11:11:37 +0200
Subject: [PATCH 04/41] Fix function name

---
 clarity_epp/export/tecan.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/clarity_epp/export/tecan.py b/clarity_epp/export/tecan.py
index a47ab2f..0eddeeb 100755
--- a/clarity_epp/export/tecan.py
+++ b/clarity_epp/export/tecan.py
@@ -5,7 +5,7 @@
 import clarity_epp.export.utils
 
 
-def samplesheet_qc(lims, process_id, type, output_file):
+def samplesheet(lims, process_id, type, output_file):
     """Create Tecan samplesheet."""
     process = Process(lims, id=process_id)
     well_plate = {}

From 43a10f9782176ce2fbed3a2a59415de7c031280d Mon Sep 17 00:00:00 2001
From: Robert Ernst <r.f.ernst-3@umcutrecht.nl>
Date: Wed, 12 Oct 2022 16:54:51 +0200
Subject: [PATCH 05/41] Add placement script for tecan

---
 clarity_epp.py                    |  9 ++++++
 clarity_epp/placement/__init__.py |  1 +
 clarity_epp/placement/tecan.py    | 50 +++++++++++++++++++++++++++++++
 3 files changed, 60 insertions(+)
 create mode 100644 clarity_epp/placement/tecan.py

diff --git a/clarity_epp.py b/clarity_epp.py
index 2c69795..a4d3fbe 100755
--- a/clarity_epp.py
+++ b/clarity_epp.py
@@ -221,6 +221,11 @@ def placement_complete_step(args):
     clarity_epp.placement.step.finish_protocol_complete(lims, args.process_id)
 
 
+def placement_tecan(args):
+    """Placement tecan process, distribute artifacts over two containers"""
+    clarity_epp.placement.tecan.place_samples(lims, args.process_id)
+
+
 if __name__ == "__main__":
     parser = argparse.ArgumentParser()
     subparser = parser.add_subparsers()
@@ -419,5 +424,9 @@ def placement_complete_step(args):
     parser_placement_unpooling.add_argument('process_id', help='Clarity lims process id')
     parser_placement_unpooling.set_defaults(func=placement_unpooling)
 
+    parser_placement_tecan = subparser_placement.add_parser('tecan', help='Placement of samples in tecan step')
+    parser_placement_tecan.add_argument('process_id', help='Clarity lims process id')
+    parser_placement_tecan.set_defaults(func=placement_tecan)
+
     args = parser.parse_args()
     args.func(args)
diff --git a/clarity_epp/placement/__init__.py b/clarity_epp/placement/__init__.py
index 6c6bff7..f5f088d 100644
--- a/clarity_epp/placement/__init__.py
+++ b/clarity_epp/placement/__init__.py
@@ -5,3 +5,4 @@
 import clarity_epp.placement.plate
 import clarity_epp.placement.pool
 import clarity_epp.placement.step
+import clarity_epp.placement.tecan
\ No newline at end of file
diff --git a/clarity_epp/placement/tecan.py b/clarity_epp/placement/tecan.py
new file mode 100644
index 0000000..ae00f07
--- /dev/null
+++ b/clarity_epp/placement/tecan.py
@@ -0,0 +1,50 @@
+from genologics.entities import Process, Container, Containertype
+
+
+def get_well_location(index):
+    locations = [
+        'A:1', 'B:1', 'C:1', 'D:1', 'E:1', 'F:1', 'G:1', 'H:1',
+        'A:2', 'B:2', 'C:2', 'D:2', 'E:2', 'F:2', 'G:2', 'H:2',
+        'A:3', 'B:3', 'C:3', 'D:3', 'E:3', 'F:3', 'G:3', 'H:3',
+        'A:4', 'B:4', 'C:4', 'D:4', 'E:4', 'F:4', 'G:4', 'H:4',
+        'A:5', 'B:5', 'C:5', 'D:5', 'E:5', 'F:5', 'G:5', 'H:5',
+        'A:6', 'B:6', 'C:6', 'D:6', 'E:6', 'F:6', 'G:6', 'H:6',
+        'A:7', 'B:7', 'C:7', 'D:7', 'E:7', 'F:7', 'G:7', 'H:7',
+        'A:8', 'B:8', 'C:8', 'D:8', 'E:8', 'F:8', 'G:8', 'H:8',
+        'A:9', 'B:9', 'C:9', 'D:9', 'E:9', 'F:9', 'G:9', 'H:9',
+        'A:10', 'B:10', 'C:10', 'D:10', 'E:10', 'F:10', 'G:10', 'H:10',
+        'A:11', 'B:11', 'C:11', 'D:11', 'E:11', 'F:11', 'G:11', 'H:11',
+        'A:12', 'B:12', 'C:12', 'D:12', 'E:12', 'F:12', 'G:12', 'H:12'
+    ]
+    return locations[index]
+
+
+def place_artifacts(lims, process_id):
+    """Place artifacts on two containers, 2 artifacts per sample."""
+    process = Process(lims, id=process_id)
+
+    # Create containers
+    well_plate = Containertype(lims, id='1')
+    purify_container = Container.create(lims, type=well_plate)
+    normalise_container = Container.create(lims, type=well_plate)
+    purify_container.name = f"zuiveren_{purify_container.name}"
+    normalise_container.name = f"normaliseren_{normalise_container.name}"
+    purify_container.put()
+    normalise_container.put()
+
+    # Keep track of placements
+    purify_container_placement = []
+    normalise_container_placement = []
+    placement_list = []
+
+    # Place all artifacts
+    for artifact in process.analytes()[0]:
+        if artifact.name not in purify_container_placement:
+            placement_list.append([artifact, (purify_container, get_well_location(len(purify_container_placement)))])
+            purify_container_placement.append(artifact.name)
+        else:
+            placement_list.append([artifact, (normalise_container, get_well_location(len(normalise_container_placement)))])
+            normalise_container_placement.append(artifact.name)
+
+    process.step.placements.set_placement_list(placement_list)
+    process.step.placements.post()

From fe7a1f802ac5707746f94089bbd8e6c2534b0570 Mon Sep 17 00:00:00 2001
From: Robert Ernst <r.f.ernst-3@umcutrecht.nl>
Date: Wed, 12 Oct 2022 16:58:07 +0200
Subject: [PATCH 06/41] Fix function name

---
 clarity_epp.py                    | 2 +-
 clarity_epp/placement/__init__.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/clarity_epp.py b/clarity_epp.py
index a4d3fbe..6f80200 100755
--- a/clarity_epp.py
+++ b/clarity_epp.py
@@ -223,7 +223,7 @@ def placement_complete_step(args):
 
 def placement_tecan(args):
     """Placement tecan process, distribute artifacts over two containers"""
-    clarity_epp.placement.tecan.place_samples(lims, args.process_id)
+    clarity_epp.placement.tecan.place_artifacts(lims, args.process_id)
 
 
 if __name__ == "__main__":
diff --git a/clarity_epp/placement/__init__.py b/clarity_epp/placement/__init__.py
index f5f088d..c9d5394 100644
--- a/clarity_epp/placement/__init__.py
+++ b/clarity_epp/placement/__init__.py
@@ -5,4 +5,4 @@
 import clarity_epp.placement.plate
 import clarity_epp.placement.pool
 import clarity_epp.placement.step
-import clarity_epp.placement.tecan
\ No newline at end of file
+import clarity_epp.placement.tecan

From 36b67b2fc29467b6c6f4512718ac684fb876176c Mon Sep 17 00:00:00 2001
From: Robert Ernst <r.f.ernst-3@umcutrecht.nl>
Date: Wed, 12 Oct 2022 16:59:43 +0200
Subject: [PATCH 07/41] Remove f string

---
 clarity_epp/placement/tecan.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/clarity_epp/placement/tecan.py b/clarity_epp/placement/tecan.py
index ae00f07..0943602 100644
--- a/clarity_epp/placement/tecan.py
+++ b/clarity_epp/placement/tecan.py
@@ -27,8 +27,8 @@ def place_artifacts(lims, process_id):
     well_plate = Containertype(lims, id='1')
     purify_container = Container.create(lims, type=well_plate)
     normalise_container = Container.create(lims, type=well_plate)
-    purify_container.name = f"zuiveren_{purify_container.name}"
-    normalise_container.name = f"normaliseren_{normalise_container.name}"
+    purify_container.name = "zuiveren_{id}".format(id=purify_container.name)
+    normalise_container.name = "normaliseren_{id}".format(id=normalise_container.name)
     purify_container.put()
     normalise_container.put()
 

From fd0b5e5377af89943f3a51ffc2361b7dcd19eb85 Mon Sep 17 00:00:00 2001
From: Robert Ernst <r.f.ernst-3@umcutrecht.nl>
Date: Thu, 13 Oct 2022 10:42:07 +0200
Subject: [PATCH 08/41] Make sure samples are set to same well location

---
 clarity_epp/placement/tecan.py | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/clarity_epp/placement/tecan.py b/clarity_epp/placement/tecan.py
index 0943602..b8a2c9b 100644
--- a/clarity_epp/placement/tecan.py
+++ b/clarity_epp/placement/tecan.py
@@ -33,18 +33,18 @@ def place_artifacts(lims, process_id):
     normalise_container.put()
 
     # Keep track of placements
-    purify_container_placement = []
-    normalise_container_placement = []
+    container_placement = {}
     placement_list = []
 
     # Place all artifacts
     for artifact in process.analytes()[0]:
-        if artifact.name not in purify_container_placement:
-            placement_list.append([artifact, (purify_container, get_well_location(len(purify_container_placement)))])
-            purify_container_placement.append(artifact.name)
-        else:
-            placement_list.append([artifact, (normalise_container, get_well_location(len(normalise_container_placement)))])
-            normalise_container_placement.append(artifact.name)
+        if artifact.name not in container_placement:  # Add first artifact to purify_container
+            well_location = get_well_location(len(container_placement))
+            placement_list.append([artifact, (purify_container, well_location)])
+            container_placement[artifact.name] = well_location
+        else:  # Add second artifact to normalise_container on same position
+            well_location = container_placement[artifact.name]
+            placement_list.append([artifact, (normalise_container, well_location)])
 
     process.step.placements.set_placement_list(placement_list)
     process.step.placements.post()

From e6553761f1c63c858c0aa7a7544b7a01298079ed Mon Sep 17 00:00:00 2001
From: Robert Ernst <r.f.ernst-3@umcutrecht.nl>
Date: Tue, 25 Oct 2022 16:04:59 +0200
Subject: [PATCH 09/41] Update tecan samplesheet

---
 clarity_epp/export/tecan.py | 21 +++++++++++++--------
 1 file changed, 13 insertions(+), 8 deletions(-)

diff --git a/clarity_epp/export/tecan.py b/clarity_epp/export/tecan.py
index 0eddeeb..b6bfd3b 100755
--- a/clarity_epp/export/tecan.py
+++ b/clarity_epp/export/tecan.py
@@ -12,23 +12,28 @@ def samplesheet(lims, process_id, type, output_file):
 
     for placement, artifact in process.output_containers()[0].placements.items():
         placement = ''.join(placement.split(':'))
-        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
+        well_plate[placement] = artifact
 
     if type == 'qc':
         output_file.write('Position\tSample\n')
         for well in clarity_epp.export.utils.sort_96_well_plate(well_plate.keys()):
-            output_file.write('{well}\t{sample}\n'.format(
+            # Set correct artifact name
+            artifact = well_plate[well]
+            if len(artifact.samples) == 1:
+                artifact_name = artifact.name.split('_')[0]
+            else:
+                artifact_name = artifact.name
+
+            output_file.write('{well}\t{artifact}\n'.format(
                 well=well,
-                sample=well_plate[well]
+                artifact=artifact_name
             ))
 
     elif type == 'purify_normalise':
-        output_file.write('Sample\tPosition\n')
+        output_file.write('SourceTubeID\tPositionID\n')
         for well in clarity_epp.export.utils.sort_96_well_plate(well_plate.keys()):
+            sample = artifact.samples[0]  # assume one sample per tube
             output_file.write('{sample}\t{well}\n'.format(
-                sample=well_plate[well],
+                sample=sample.udf['Dx Fractienummer'],
                 well=well
             ))
\ No newline at end of file

From 06affc5342cda01626d6be9827cbd94c6c8fef6a Mon Sep 17 00:00:00 2001
From: Robert Ernst <r.f.ernst-3@umcutrecht.nl>
Date: Tue, 25 Oct 2022 16:21:36 +0200
Subject: [PATCH 10/41] Use final_volume to correct for s1/s2/s4 volume
 differences

---
 clarity_epp/export/manual_pipetting.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/clarity_epp/export/manual_pipetting.py b/clarity_epp/export/manual_pipetting.py
index 70a2dd4..01dbf5d 100755
--- a/clarity_epp/export/manual_pipetting.py
+++ b/clarity_epp/export/manual_pipetting.py
@@ -311,6 +311,7 @@ def samplesheet_multiplex_sequence_pool(lims, process_id, output_file):
     input_pools = []
     total_sample_count = 0
     total_load_uL = 0
+    final_volume = float(process.udf['Final volume'].split()[0])
 
     for input_pool in process.all_inputs():
         input_pool_conc = float(input_pool.udf['Dx Concentratie fluorescentie (ng/ul)'])
@@ -339,11 +340,11 @@ def samplesheet_multiplex_sequence_pool(lims, process_id, output_file):
     # Last calcuations and print sample
     for input_pool in input_pools:
         input_pool_load_pM = (float(process.udf['Dx Laadconcentratie (pM)'])/total_sample_count) * input_pool['sample_count']
-        input_pool_load_uL = 150.0 / (input_pool['pM']/input_pool_load_pM)
+        input_pool_load_uL = final_volume / (input_pool['pM']/input_pool_load_pM)
         total_load_uL += input_pool_load_uL
         output_file.write('{0}\t{1:.2f}\n'.format(input_pool['name'], input_pool_load_uL))
 
-    tris_HCL_uL = 150 - total_load_uL
+    tris_HCL_uL = final_volume - total_load_uL
     output_file.write('{0}\t{1:.2f}\n'.format('Tris-HCL', tris_HCL_uL))
 
 

From d69a47aa6a9b21e58394ccd9a766576099b283ce Mon Sep 17 00:00:00 2001
From: Robert Ernst <r.f.ernst-3@umcutrecht.nl>
Date: Tue, 25 Oct 2022 16:52:15 +0200
Subject: [PATCH 11/41] Update overmaat to 30%

---
 clarity_epp/export/manual_pipetting.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/clarity_epp/export/manual_pipetting.py b/clarity_epp/export/manual_pipetting.py
index 01dbf5d..6917034 100755
--- a/clarity_epp/export/manual_pipetting.py
+++ b/clarity_epp/export/manual_pipetting.py
@@ -456,11 +456,11 @@ def sammplesheet_exonuclease(lims, process_id, output_file):
 
     # Caculate for sample count
     for i, item in enumerate(data):
-        data[i].append(sample_count * item[1] * 1.25)
+        data[i].append(sample_count * item[1] * 1.30)
 
     # Calculate total
     data.append([
-        'TOTAL (incl. 25% overmaat)',
+        'TOTAL (incl. 30% overmaat)',
         sum([item[1] for item in data]),
         sum([item[2] for item in data]),
     ])

From 3c29bfa60089f7450486166aec463c16cee90e72 Mon Sep 17 00:00:00 2001
From: Robert Ernst <r.f.ernst-3@umcutrecht.nl>
Date: Tue, 25 Oct 2022 16:55:17 +0200
Subject: [PATCH 12/41] Update volume mip_multiplex_pool

---
 clarity_epp/export/manual_pipetting.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/clarity_epp/export/manual_pipetting.py b/clarity_epp/export/manual_pipetting.py
index 6917034..6bba8c5 100755
--- a/clarity_epp/export/manual_pipetting.py
+++ b/clarity_epp/export/manual_pipetting.py
@@ -556,9 +556,9 @@ def samplesheet_mip_multiplex_pool(lims, process_id, output_file):
         if input_artifact['concentration'] < avg_concentration * 0.5:
             input_artifact['volume'] = 20
         elif input_artifact['concentration'] > avg_concentration * 1.5:
-            input_artifact['volume'] = 2
+            input_artifact['volume'] = 1
         else:
-            input_artifact['volume'] = 5
+            input_artifact['volume'] = 2
 
         if input_artifact['plate_id'] not in input_containers:
             input_containers[input_artifact['plate_id']] = {}

From b4832ac320315428f2fd82e126245a5c03a38a5c Mon Sep 17 00:00:00 2001
From: Robert Ernst <r.f.ernst-3@umcutrecht.nl>
Date: Thu, 27 Oct 2022 15:18:13 +0200
Subject: [PATCH 13/41] Update storage location label

---
 clarity_epp/export/labels.py | 13 ++++++++-----
 1 file changed, 8 insertions(+), 5 deletions(-)

diff --git a/clarity_epp/export/labels.py b/clarity_epp/export/labels.py
index a514fb0..f63ae8f 100644
--- a/clarity_epp/export/labels.py
+++ b/clarity_epp/export/labels.py
@@ -30,10 +30,13 @@ def container_sample(lims, process_id, output_file, description=''):
 def storage_location(lims, process_id, output_file):
     """Generate storage location label file."""
     process = Process(lims, id=process_id)
+
+    # Write header
+    output_file.write('Bakje\tpos\n')
+
     for artifact in process.analytes()[0]:
-        storage_location = artifact.samples[0].udf['Dx Opslaglocatie']
-        output_file.write('{sample}\t{storage_location}\t{birth_date}\n'.format(
-            sample=artifact.samples[0].name,
-            storage_location=storage_location,
-            birth_date=artifact.samples[0].udf['Dx Geboortejaar']
+        storage_location = artifact.samples[0].udf['Dx Opslaglocatie'].split()
+        output_file.write('{tray}\t{pos}\n'.format(
+            tray=storage_location[0][2:6],  # Select 4 digits from: CB[1-9][1-9][1-9][1-9]KK
+            pos=storage_location[1]
         ))

From 7fe5b52f601369b807448211be8a44d46f7709c8 Mon Sep 17 00:00:00 2001
From: Robert Ernst <r.f.ernst-3@umcutrecht.nl>
Date: Fri, 28 Oct 2022 15:24:31 +0200
Subject: [PATCH 14/41] pep8

---
 clarity_epp/export/utils.py | 17 ++++++++++++-----
 1 file changed, 12 insertions(+), 5 deletions(-)

diff --git a/clarity_epp/export/utils.py b/clarity_epp/export/utils.py
index 7bf6a25..4132edd 100755
--- a/clarity_epp/export/utils.py
+++ b/clarity_epp/export/utils.py
@@ -9,11 +9,18 @@ def sort_96_well_plate(wells):
 
     """
     order = [
-        'A1', 'B1', 'C1', 'D1', 'E1', 'F1', 'G1', 'H1', 'A2', 'B2', 'C2', 'D2', 'E2', 'F2', 'G2', 'H2', 'A3', 'B3', 'C3', 'D3', 'E3', 'F3', 'G3',
-        'H3', 'A4', 'B4', 'C4', 'D4', 'E4', 'F4', 'G4', 'H4', 'A5', 'B5', 'C5', 'D5', 'E5', 'F5', 'G5', 'H5', 'A6', 'B6', 'C6', 'D6', 'E6', 'F6',
-        'G6', 'H6', 'A7', 'B7', 'C7', 'D7', 'E7', 'F7', 'G7', 'H7', 'A8', 'B8', 'C8', 'D8', 'E8', 'F8', 'G8', 'H8', 'A9', 'B9', 'C9', 'D9', 'E9',
-        'F9', 'G9', 'H9', 'A10', 'B10', 'C10', 'D10', 'E10', 'F10', 'G10', 'H10', 'A11', 'B11', 'C11', 'D11', 'E11', 'F11', 'G11', 'H11', 'A12',
-        'B12', 'C12', 'D12', 'E12', 'F12', 'G12', 'H12'
+        'A1', 'B1', 'C1', 'D1', 'E1', 'F1', 'G1', 'H1',
+        'A2', 'B2', 'C2', 'D2', 'E2', 'F2', 'G2', 'H2',
+        'A3', 'B3', 'C3', 'D3', 'E3', 'F3', 'G3', 'H3',
+        'A4', 'B4', 'C4', 'D4', 'E4', 'F4', 'G4', 'H4',
+        'A5', 'B5', 'C5', 'D5', 'E5', 'F5', 'G5', 'H5',
+        'A6', 'B6', 'C6', 'D6', 'E6', 'F6', 'G6', 'H6',
+        'A7', 'B7', 'C7', 'D7', 'E7', 'F7', 'G7', 'H7',
+        'A8', 'B8', 'C8', 'D8', 'E8', 'F8', 'G8', 'H8',
+        'A9', 'B9', 'C9', 'D9', 'E9', 'F9', 'G9', 'H9',
+        'A10', 'B10', 'C10', 'D10', 'E10', 'F10', 'G10', 'H10',
+        'A11', 'B11', 'C11', 'D11', 'E11', 'F11', 'G11', 'H11',
+        'A12', 'B12', 'C12', 'D12', 'E12', 'F12', 'G12', 'H12'
     ]
     order = dict(zip(order, range(len(order))))
 

From 3ca901d00ef8a17d95ceab6b8bdeed3b49c2ca34 Mon Sep 17 00:00:00 2001
From: Robert Ernst <r.f.ernst-3@umcutrecht.nl>
Date: Fri, 28 Oct 2022 15:30:41 +0200
Subject: [PATCH 15/41] Add index

---
 clarity_epp/export/tecan.py |  7 ++++---
 clarity_epp/export/utils.py | 28 ++++++++++++++++++++++++++++
 2 files changed, 32 insertions(+), 3 deletions(-)

diff --git a/clarity_epp/export/tecan.py b/clarity_epp/export/tecan.py
index b6bfd3b..54bc0de 100755
--- a/clarity_epp/export/tecan.py
+++ b/clarity_epp/export/tecan.py
@@ -30,10 +30,11 @@ def samplesheet(lims, process_id, type, output_file):
             ))
 
     elif type == 'purify_normalise':
-        output_file.write('SourceTubeID\tPositionID\n')
+        output_file.write('SourceTubeID\tPositionID\tPositionIndex\n')
         for well in clarity_epp.export.utils.sort_96_well_plate(well_plate.keys()):
             sample = artifact.samples[0]  # assume one sample per tube
-            output_file.write('{sample}\t{well}\n'.format(
+            output_file.write('{sample}\t{well}\t{index}\n'.format(
                 sample=sample.udf['Dx Fractienummer'],
-                well=well
+                well=well,
+                index=clarity_epp.export.utils.get_well_index(well, one_based=True)
             ))
\ No newline at end of file
diff --git a/clarity_epp/export/utils.py b/clarity_epp/export/utils.py
index 4132edd..1f9d20c 100755
--- a/clarity_epp/export/utils.py
+++ b/clarity_epp/export/utils.py
@@ -56,3 +56,31 @@ def get_process_types(lims, process_types_names):
                 process_types.append(process_type.name)
 
     return process_types
+
+
+def get_well_index(well, one_based=False):
+    """Return well index
+
+    Arguments:
+    well -- well str: 'A1'
+
+    """
+    wells = [
+        'A1', 'B1', 'C1', 'D1', 'E1', 'F1', 'G1', 'H1',
+        'A2', 'B2', 'C2', 'D2', 'E2', 'F2', 'G2', 'H2',
+        'A3', 'B3', 'C3', 'D3', 'E3', 'F3', 'G3', 'H3',
+        'A4', 'B4', 'C4', 'D4', 'E4', 'F4', 'G4', 'H4',
+        'A5', 'B5', 'C5', 'D5', 'E5', 'F5', 'G5', 'H5',
+        'A6', 'B6', 'C6', 'D6', 'E6', 'F6', 'G6', 'H6',
+        'A7', 'B7', 'C7', 'D7', 'E7', 'F7', 'G7', 'H7',
+        'A8', 'B8', 'C8', 'D8', 'E8', 'F8', 'G8', 'H8',
+        'A9', 'B9', 'C9', 'D9', 'E9', 'F9', 'G9', 'H9',
+        'A10', 'B10', 'C10', 'D10', 'E10', 'F10', 'G10', 'H10',
+        'A11', 'B11', 'C11', 'D11', 'E11', 'F11', 'G11', 'H11',
+        'A12', 'B12', 'C12', 'D12', 'E12', 'F12', 'G12', 'H12'
+    ]
+
+    if one_based:
+        return wells.index(well) + 1
+    else:
+        return wells.index(well)

From 009a6ea608b426fd9f0fb49eaf84381c4c6fe7ee Mon Sep 17 00:00:00 2001
From: Robert Ernst <r.f.ernst-3@umcutrecht.nl>
Date: Tue, 8 Nov 2022 12:45:29 +0100
Subject: [PATCH 16/41] Fix trio parsing

---
 clarity_epp/placement/artifact.py | 21 +++++++++++++++++----
 1 file changed, 17 insertions(+), 4 deletions(-)

diff --git a/clarity_epp/placement/artifact.py b/clarity_epp/placement/artifact.py
index fb028a7..8963ea7 100644
--- a/clarity_epp/placement/artifact.py
+++ b/clarity_epp/placement/artifact.py
@@ -54,12 +54,25 @@ def route_to_workflow(lims, process_id, workflow):
 
             # Remove research artifacts
             if sample.udf['Dx Stoftest code'] != config.stoftestcode_research:
-                # Find trio
-                if(
-                    sample.udf['Dx Familie status'] == 'Ouder'
-                    or ('Dx Gerelateerde onderzoeken' in sample.udf and sample.udf['Dx Gerelateerde onderzoeken'])
+                # Lookup trio samples
+                # if parent check family members if parent belongs to trio
+                if sample.udf['Dx Familie status'] == 'Ouder':
+                    parent_status = 'single'
+                    for family_sample in lims.get_samples(udf={'Dx Familienummer': sample.udf['Dx Familienummer']}):
+                        if(
+                            'Dx Gerelateerde onderzoeken' in family_sample.udf
+                            and sample.udf['Dx Onderzoeknummer'] in family_sample.udf['Dx Gerelateerde onderzoeken']
+                            and len(family_sample.udf['Dx Gerelateerde onderzoeken'].split(';')) >= 2
+                        ):
+                            parent_status = 'trio'
+                    stoftest_artifacts[sample.udf['Dx Stoftest code']][parent_status].append(artifact)
+                # If child check if part of trio
+                elif(
+                    'Dx Gerelateerde onderzoeken' in sample.udf
+                    and len(sample.udf['Dx Gerelateerde onderzoeken'].split(';')) >= 2
                 ):
                     stoftest_artifacts[sample.udf['Dx Stoftest code']]['trio'].append(artifact)
+                # Else not trio
                 else:
                     stoftest_artifacts[sample.udf['Dx Stoftest code']]['single'].append(artifact)
 

From 4cc9735ffc8f9b14e5baf4fcfa3d5f1ed07385fe Mon Sep 17 00:00:00 2001
From: Robert Ernst <r.f.ernst-3@umcutrecht.nl>
Date: Tue, 8 Nov 2022 12:53:09 +0100
Subject: [PATCH 17/41] Sort magnis pools by id

---
 clarity_epp/export/manual_pipetting.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/clarity_epp/export/manual_pipetting.py b/clarity_epp/export/manual_pipetting.py
index 6bba8c5..2ca0b0f 100755
--- a/clarity_epp/export/manual_pipetting.py
+++ b/clarity_epp/export/manual_pipetting.py
@@ -668,7 +668,7 @@ def samplesheet_pool_magnis_pools(lims, process_id, output_file):
     output_file.write('Pool\tContainer\tSample count\tVolume (ul)\n')
 
     # Get input pools, sort by name and print volume
-    for input_artifact in sorted(process.all_inputs(resolve=True), key=lambda artifact: artifact.name):
+    for input_artifact in sorted(process.all_inputs(resolve=True), key=lambda artifact: artifact.id):
         sample_count = 0
         for sample in input_artifact.samples:
             if 'Dx Exoomequivalent' in sample.udf:

From 64e25f546193b201f29200aab0354f27640e76f6 Mon Sep 17 00:00:00 2001
From: Robert Ernst <r.f.ernst-3@umcutrecht.nl>
Date: Thu, 24 Nov 2022 11:37:54 +0100
Subject: [PATCH 18/41] Fix samplesheet

---
 clarity_epp/export/tecan.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/clarity_epp/export/tecan.py b/clarity_epp/export/tecan.py
index 54bc0de..c9c3c41 100755
--- a/clarity_epp/export/tecan.py
+++ b/clarity_epp/export/tecan.py
@@ -32,6 +32,7 @@ def samplesheet(lims, process_id, type, output_file):
     elif type == 'purify_normalise':
         output_file.write('SourceTubeID\tPositionID\tPositionIndex\n')
         for well in clarity_epp.export.utils.sort_96_well_plate(well_plate.keys()):
+            artifact = well_plate[well]
             sample = artifact.samples[0]  # assume one sample per tube
             output_file.write('{sample}\t{well}\t{index}\n'.format(
                 sample=sample.udf['Dx Fractienummer'],

From 8149a488c37e2de5c87f737a24cd99df99d69034 Mon Sep 17 00:00:00 2001
From: Robert Ernst <r.f.ernst-3@umcutrecht.nl>
Date: Thu, 24 Nov 2022 13:44:03 +0100
Subject: [PATCH 19/41] Add results_purify_normalise

---
 clarity_epp.py                |  6 +++++-
 clarity_epp/upload/samples.py |  2 +-
 clarity_epp/upload/tecan.py   | 30 +++++++++++++++++++++++++++++-
 clarity_epp/upload/utils.py   | 12 ++++++++----
 4 files changed, 43 insertions(+), 7 deletions(-)

diff --git a/clarity_epp.py b/clarity_epp.py
index 6f80200..dfc4ee6 100755
--- a/clarity_epp.py
+++ b/clarity_epp.py
@@ -147,7 +147,10 @@ def upload_samples(args):
 
 def upload_tecan_results(args):
     """Upload tecan results."""
-    clarity_epp.upload.tecan.results(lims, args.process_id)
+    if args.type == 'qc':
+        clarity_epp.upload.tecan.results_qc(lims, args.process_id)
+    elif args.type == 'purify_normalise':
+        clarity_epp.upload.tecan.results_purify_normalise(lims, args.process_id)
 
 
 def upload_tapestation_results(args):
@@ -363,6 +366,7 @@ def placement_tecan(args):
 
     parser_upload_tecan = subparser_upload.add_parser('tecan', help='Upload tecan results')
     parser_upload_tecan.add_argument('process_id', help='Clarity lims process id')
+    parser_upload_tecan.add_argument('type', choices=['qc', 'purify_normalise'], help='Tecan process type')
     parser_upload_tecan.set_defaults(func=upload_tecan_results)
 
     parser_upload_magnis = subparser_upload.add_parser('magnis', help='Upload magnis results')
diff --git a/clarity_epp/upload/samples.py b/clarity_epp/upload/samples.py
index 48c7ceb..ae42af0 100644
--- a/clarity_epp/upload/samples.py
+++ b/clarity_epp/upload/samples.py
@@ -91,7 +91,7 @@ def from_helix(lims, email_settings, input_file):
         for udf in udf_column:
             # Transform specific udf
             if udf in ['Dx Overleden', 'Dx Spoed', 'Dx NICU Spoed']:
-                udf_data[udf] = clarity_epp.upload.utils.char_to_bool(data[udf_column[udf]['index']])
+                udf_data[udf] = clarity_epp.upload.utils.txt_to_bool(data[udf_column[udf]['index']])
             elif udf in ['Dx Geslacht', 'Dx Foetus geslacht']:
                 udf_data[udf] = clarity_epp.upload.utils.transform_sex(data[udf_column[udf]['index']])
             elif udf == 'Dx Foetus':
diff --git a/clarity_epp/upload/tecan.py b/clarity_epp/upload/tecan.py
index 4ab8222..712105d 100644
--- a/clarity_epp/upload/tecan.py
+++ b/clarity_epp/upload/tecan.py
@@ -4,8 +4,10 @@
 
 from genologics.entities import Process
 
+from clarity_epp.upload.utils import txt_to_bool
 
-def results(lims, process_id):
+
+def results_qc(lims, process_id):
     """Upload tecan results to artifacts."""
     process = Process(lims, id=process_id)
     concentration_range = map(float, re.findall('[\d\.]+', process.udf['Concentratiebereik (ng/ul)']))
@@ -108,3 +110,29 @@ def results(lims, process_id):
                     artifact.qc_flag = 'FAILED'
 
             artifact.put()
+
+
+def results_purify_normalise(lims, process_id):
+    """Upload tecan results to artifacts."""
+    process = Process(lims, id=process_id)
+
+    # Find and parse Tecan Fluent 480 Output
+    tecan_result = {}
+    for result_file in process.result_files():
+        if result_file.name == 'Tecan Fluent 480 Output':
+            file_data = lims.get_file_contents(result_file.files[0].id).split('\n')
+            header = file_data[0].rstrip().split(',')
+            for line in file_data[1:]:
+                data = line.rstrip().split(',')
+                tecan_result[data[header.index('SampleID')]] = {
+                    'conc': float(data[header.index('Concentratie')]),
+                    'norm': txt_to_bool(data[header.index('Normalisatie')])
+                }
+            break  # File found exit loop
+
+    # Set concentration values on artifacts
+    for artifact in process.analytes()[0]:
+        sample = artifact.samples[0]  # assume one sample per artifact
+        artifact.udf['Dx Concentratie fluorescentie (ng/ul)'] = tecan_result[sample.udf['Dx Fractienummer']]['conc']
+        artifact.udf['Dx QC status'] = tecan_result[sample.udf['Dx Fractienummer']]['norm']
+        artifact.put()
diff --git a/clarity_epp/upload/utils.py b/clarity_epp/upload/utils.py
index 6b2078b..cb35aa3 100644
--- a/clarity_epp/upload/utils.py
+++ b/clarity_epp/upload/utils.py
@@ -4,14 +4,18 @@
 import config
 
 
-def char_to_bool(letter):
+def txt_to_bool(txt):
     """Transform character (J/N) to Bool."""
-    if letter.upper() == 'J':
+    if txt.upper() == 'J':
         return True
-    elif letter.upper() == 'N':
+    elif txt.upper() == 'N':
+        return False
+    elif txt.upper() == "TRUE":
+        return True
+    elif txt.upper() == "FALSE":
         return False
     else:
-        raise ValueError('Invalid character, only J or N allowed.')
+        raise ValueError('Invalid text, only J, N, TRUE or FALSE allowed.')
 
 
 def transform_sex(value):

From 0ca569dda2cea9e5a8884b8adb0034442aee0dde Mon Sep 17 00:00:00 2001
From: Robert Ernst <r.f.ernst-3@umcutrecht.nl>
Date: Thu, 24 Nov 2022 13:55:13 +0100
Subject: [PATCH 20/41] pep8

---
 clarity_epp/export/tecan.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/clarity_epp/export/tecan.py b/clarity_epp/export/tecan.py
index c9c3c41..ccc9d34 100755
--- a/clarity_epp/export/tecan.py
+++ b/clarity_epp/export/tecan.py
@@ -38,4 +38,4 @@ def samplesheet(lims, process_id, type, output_file):
                 sample=sample.udf['Dx Fractienummer'],
                 well=well,
                 index=clarity_epp.export.utils.get_well_index(well, one_based=True)
-            ))
\ No newline at end of file
+            ))

From cf8581d5e88e73c5a43a0f933a1a5c78756534d8 Mon Sep 17 00:00:00 2001
From: Robert Ernst <r.f.ernst-3@umcutrecht.nl>
Date: Thu, 24 Nov 2022 14:54:33 +0100
Subject: [PATCH 21/41] Change seperator

---
 clarity_epp/upload/tecan.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/clarity_epp/upload/tecan.py b/clarity_epp/upload/tecan.py
index 712105d..a10db71 100644
--- a/clarity_epp/upload/tecan.py
+++ b/clarity_epp/upload/tecan.py
@@ -121,9 +121,9 @@ def results_purify_normalise(lims, process_id):
     for result_file in process.result_files():
         if result_file.name == 'Tecan Fluent 480 Output':
             file_data = lims.get_file_contents(result_file.files[0].id).split('\n')
-            header = file_data[0].rstrip().split(',')
+            header = file_data[0].rstrip().split(';')
             for line in file_data[1:]:
-                data = line.rstrip().split(',')
+                data = line.rstrip().split(';')
                 tecan_result[data[header.index('SampleID')]] = {
                     'conc': float(data[header.index('Concentratie')]),
                     'norm': txt_to_bool(data[header.index('Normalisatie')])

From f685524f67c0a90ee514861d7e59c1b7d9f4f91d Mon Sep 17 00:00:00 2001
From: Robert Ernst <r.f.ernst-3@umcutrecht.nl>
Date: Thu, 24 Nov 2022 16:04:05 +0100
Subject: [PATCH 22/41] Add tests for utils

---
 .github/workflows/python.yml | 44 ++++++++++++++++++++++++++++++++++++
 tests/__init__.py            |  0
 tests/test_export_utils.py   | 23 +++++++++++++++++++
 tests/test_upload_utils.py   | 18 +++++++++++++++
 4 files changed, 85 insertions(+)
 create mode 100644 .github/workflows/python.yml
 create mode 100644 tests/__init__.py
 create mode 100644 tests/test_export_utils.py
 create mode 100644 tests/test_upload_utils.py

diff --git a/.github/workflows/python.yml b/.github/workflows/python.yml
new file mode 100644
index 0000000..227ceca
--- /dev/null
+++ b/.github/workflows/python.yml
@@ -0,0 +1,44 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Python (flake8, pytest)
+
+on:
+  push:
+    branches: [main, develop]
+  pull_request:
+    branches: [main, develop]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: [3.6]
+
+    steps:
+    - uses: actions/checkout@v3
+      with:
+        fetch-depth: 0
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v3
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: "Install Apache package"
+      run: sudo apt install -y apache2-dev
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install flake8 pytest
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+    - name: Lint with flake8
+      run: |
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: Test with pytest
+      run: |
+        pytest
\ No newline at end of file
diff --git a/tests/__init__.py b/tests/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/tests/test_export_utils.py b/tests/test_export_utils.py
new file mode 100644
index 0000000..70bfea8
--- /dev/null
+++ b/tests/test_export_utils.py
@@ -0,0 +1,23 @@
+from genologics.lims import Lims
+from genologics.entities import Artifact
+
+from clarity_epp.export import utils
+
+
+def test_sort_96_well_plate():
+    assert utils.sort_96_well_plate(['B2', 'A1', 'E1']) == ['A1', 'E1', 'B2']
+
+
+def test_reverse_complement():
+    assert utils.reverse_complement('CGTA') == 'TACG'
+
+
+def test_sort_artifact_list():
+    lims = Lims('url', username='test', password='password')
+    artifact = Artifact(lims, id='12-456')
+    assert utils.sort_artifact_list(artifact) == 456
+
+
+def test_get_well_index():
+    assert utils.get_well_index('A1') == 0
+    assert utils.get_well_index('A1', one_based=True) == 1
diff --git a/tests/test_upload_utils.py b/tests/test_upload_utils.py
new file mode 100644
index 0000000..f816eec
--- /dev/null
+++ b/tests/test_upload_utils.py
@@ -0,0 +1,18 @@
+from clarity_epp.upload import utils
+
+
+def test_txt_to_bool():
+    assert utils.txt_to_bool('J')
+    assert not utils.txt_to_bool('N')
+    assert utils.txt_to_bool('TRUE')
+    assert not utils.txt_to_bool('FALSE')
+
+
+def test_transform_sex():
+    assert utils.transform_sex('M') == 'Man'
+    assert utils.transform_sex('V') == 'Vrouw'
+    assert utils.transform_sex('O') == 'Onbekend'
+
+
+def test_transform_sample_name():
+    assert utils.transform_sample_name('D01/2016') == 'D012016'

From 91ce163218db48045aedace5c0d854b31836053d Mon Sep 17 00:00:00 2001
From: Robert Ernst <r.f.ernst-3@umcutrecht.nl>
Date: Tue, 17 Jan 2023 11:18:41 +0100
Subject: [PATCH 23/41] Replace special chars with '-'

---
 templates/NovaSeq_BCL2FASTQ_Reverse_Complement_Samplesheet.csv | 2 +-
 templates/NovaSeq_BCL2FASTQ_Samplesheet.csv                    | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/templates/NovaSeq_BCL2FASTQ_Reverse_Complement_Samplesheet.csv b/templates/NovaSeq_BCL2FASTQ_Reverse_Complement_Samplesheet.csv
index e0eb5a8..67ca2ff 100644
--- a/templates/NovaSeq_BCL2FASTQ_Reverse_Complement_Samplesheet.csv
+++ b/templates/NovaSeq_BCL2FASTQ_Reverse_Complement_Samplesheet.csv
@@ -57,7 +57,7 @@ if (index > 0) {
 }
 
 ${SAMPLE.NAME##NoSpecialCharacters}
-return token.replaceAll(\"[^a-zA-Z0-9_]\", \"_\")
+return token.replaceAll(\"[^a-zA-Z0-9\\_]\", \"-\")
 
 ${SAMPLE.PROJECT.NAME##NoSpecialCharacters}
 return token.replaceAll(\"[^a-zA-Z0-9_]\", \"_\")
diff --git a/templates/NovaSeq_BCL2FASTQ_Samplesheet.csv b/templates/NovaSeq_BCL2FASTQ_Samplesheet.csv
index cf86d3d..f7f1936 100644
--- a/templates/NovaSeq_BCL2FASTQ_Samplesheet.csv
+++ b/templates/NovaSeq_BCL2FASTQ_Samplesheet.csv
@@ -50,7 +50,7 @@ if (index >= 0) {
 }
 
 ${SAMPLE.NAME##NoSpecialCharacters}
-return token.replaceAll(\"[^a-zA-Z0-9_]\", \"_\")
+return token.replaceAll(\"[^a-zA-Z0-9\\_]\", \"-\")
 
 ${SAMPLE.PROJECT.NAME##NoSpecialCharacters}
 return token.replaceAll(\"[^a-zA-Z0-9_]\", \"_\")

From 4f6b4d624ae694fce93c40ecea481c9776896089 Mon Sep 17 00:00:00 2001
From: Robert Ernst <r.f.ernst-3@umcutrecht.nl>
Date: Tue, 17 Jan 2023 11:23:58 +0100
Subject: [PATCH 24/41] Replace special chars with '-'

---
 templates/NovaSeq_BCL2FASTQ_Reverse_Complement_Samplesheet.csv | 2 +-
 templates/NovaSeq_BCL2FASTQ_Samplesheet.csv                    | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/templates/NovaSeq_BCL2FASTQ_Reverse_Complement_Samplesheet.csv b/templates/NovaSeq_BCL2FASTQ_Reverse_Complement_Samplesheet.csv
index 67ca2ff..f2daab9 100644
--- a/templates/NovaSeq_BCL2FASTQ_Reverse_Complement_Samplesheet.csv
+++ b/templates/NovaSeq_BCL2FASTQ_Reverse_Complement_Samplesheet.csv
@@ -57,7 +57,7 @@ if (index > 0) {
 }
 
 ${SAMPLE.NAME##NoSpecialCharacters}
-return token.replaceAll(\"[^a-zA-Z0-9\\_]\", \"-\")
+return token.replaceAll(\"[^a-zA-Z0-9\\-]\", \"-\")
 
 ${SAMPLE.PROJECT.NAME##NoSpecialCharacters}
 return token.replaceAll(\"[^a-zA-Z0-9_]\", \"_\")
diff --git a/templates/NovaSeq_BCL2FASTQ_Samplesheet.csv b/templates/NovaSeq_BCL2FASTQ_Samplesheet.csv
index f7f1936..49ab47e 100644
--- a/templates/NovaSeq_BCL2FASTQ_Samplesheet.csv
+++ b/templates/NovaSeq_BCL2FASTQ_Samplesheet.csv
@@ -50,7 +50,7 @@ if (index >= 0) {
 }
 
 ${SAMPLE.NAME##NoSpecialCharacters}
-return token.replaceAll(\"[^a-zA-Z0-9\\_]\", \"-\")
+return token.replaceAll(\"[^a-zA-Z0-9\\-]\", \"-\")
 
 ${SAMPLE.PROJECT.NAME##NoSpecialCharacters}
 return token.replaceAll(\"[^a-zA-Z0-9_]\", \"_\")

From e731b58fd2780cc4550578dbd0ae333d2e6a0985 Mon Sep 17 00:00:00 2001
From: Robert Ernst <r.f.ernst-3@umcutrecht.nl>
Date: Tue, 17 Jan 2023 11:27:52 +0100
Subject: [PATCH 25/41] Replace special chars with '-'

---
 templates/NovaSeq_BCL2FASTQ_Reverse_Complement_Samplesheet.csv | 2 +-
 templates/NovaSeq_BCL2FASTQ_Samplesheet.csv                    | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/templates/NovaSeq_BCL2FASTQ_Reverse_Complement_Samplesheet.csv b/templates/NovaSeq_BCL2FASTQ_Reverse_Complement_Samplesheet.csv
index f2daab9..cd08a8e 100644
--- a/templates/NovaSeq_BCL2FASTQ_Reverse_Complement_Samplesheet.csv
+++ b/templates/NovaSeq_BCL2FASTQ_Reverse_Complement_Samplesheet.csv
@@ -57,7 +57,7 @@ if (index > 0) {
 }
 
 ${SAMPLE.NAME##NoSpecialCharacters}
-return token.replaceAll(\"[^a-zA-Z0-9\\-]\", \"-\")
+return token.replaceAll(\"[^a-zA-Z0-9-]\", \"-\")
 
 ${SAMPLE.PROJECT.NAME##NoSpecialCharacters}
 return token.replaceAll(\"[^a-zA-Z0-9_]\", \"_\")
diff --git a/templates/NovaSeq_BCL2FASTQ_Samplesheet.csv b/templates/NovaSeq_BCL2FASTQ_Samplesheet.csv
index 49ab47e..cc02f7f 100644
--- a/templates/NovaSeq_BCL2FASTQ_Samplesheet.csv
+++ b/templates/NovaSeq_BCL2FASTQ_Samplesheet.csv
@@ -50,7 +50,7 @@ if (index >= 0) {
 }
 
 ${SAMPLE.NAME##NoSpecialCharacters}
-return token.replaceAll(\"[^a-zA-Z0-9\\-]\", \"-\")
+return token.replaceAll(\"[^a-zA-Z0-9-]\", \"-\")
 
 ${SAMPLE.PROJECT.NAME##NoSpecialCharacters}
 return token.replaceAll(\"[^a-zA-Z0-9_]\", \"_\")

From 6b3274b03648b80eba94a08e822d93527ebd9ecc Mon Sep 17 00:00:00 2001
From: Robert Ernst <r.f.ernst-3@umcutrecht.nl>
Date: Tue, 17 Jan 2023 12:07:47 +0100
Subject: [PATCH 26/41] Fallback on previous process if qc process not found

---
 clarity_epp/export/manual_pipetting.py | 17 ++++++++++++-----
 1 file changed, 12 insertions(+), 5 deletions(-)

diff --git a/clarity_epp/export/manual_pipetting.py b/clarity_epp/export/manual_pipetting.py
index 2ca0b0f..d9a1346 100755
--- a/clarity_epp/export/manual_pipetting.py
+++ b/clarity_epp/export/manual_pipetting.py
@@ -364,13 +364,19 @@ def samplesheet_normalization(lims, process_id, output_file):
         sample = input_artifact.samples[0]  # asume one sample per input artifact
 
         # Find last qc process for artifact
-        qc_process = sorted(
-            lims.get_processes(type=qc_process_types, inputartifactlimsid=input_artifact.id),
-            key=lambda process: int(process.id.split('-')[-1])
-        )[-1]
+        qc_process = lims.get_processes(type=qc_process_types, inputartifactlimsid=input_artifact.id)
+        if qc_process:
+            qc_process = sorted(
+                lims.get_processes(type=qc_process_types, inputartifactlimsid=input_artifact.id),
+                key=lambda process: int(process.id.split('-')[-1])
+            )[-1]
+            qc_artifacts = qc_process.outputs_per_input(input_artifact.id)
+        else:  # Fallback on previous process if qc process not found.
+            qc_process = input_artifact.parent_process
+            qc_artifacts = qc_process.all_outputs()
 
         # Find concentration measurement
-        for qc_artifact in qc_process.outputs_per_input(input_artifact.id):
+        for qc_artifact in qc_artifacts:
             if qc_artifact.name.split(' ')[0] == artifact.name:
                 concentration = float(qc_artifact.udf['Dx Concentratie fluorescentie (ng/ul)'])
 
@@ -378,6 +384,7 @@ def samplesheet_normalization(lims, process_id, output_file):
         input_ng = float(artifact.udf['Dx Input (ng)'])
         if 'Dx pipetteervolume (ul)' in artifact.udf:
             input_ng = concentration * float(artifact.udf['Dx pipetteervolume (ul)'])
+
         sample_volume = input_ng / concentration
         water_volume = final_volume - sample_volume
         evaporate = 'N'

From aa8ca48cd753a83328648e3f878d283d9878019e Mon Sep 17 00:00:00 2001
From: Robert Ernst <r.f.ernst-3@umcutrecht.nl>
Date: Tue, 17 Jan 2023 15:26:26 +0100
Subject: [PATCH 27/41] Change output to csv

---
 clarity_epp/export/tecan.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/clarity_epp/export/tecan.py b/clarity_epp/export/tecan.py
index ccc9d34..1b61de0 100755
--- a/clarity_epp/export/tecan.py
+++ b/clarity_epp/export/tecan.py
@@ -30,11 +30,11 @@ def samplesheet(lims, process_id, type, output_file):
             ))
 
     elif type == 'purify_normalise':
-        output_file.write('SourceTubeID\tPositionID\tPositionIndex\n')
+        output_file.write('SourceTubeID,PositionID,PositionIndex\n')
         for well in clarity_epp.export.utils.sort_96_well_plate(well_plate.keys()):
             artifact = well_plate[well]
             sample = artifact.samples[0]  # assume one sample per tube
-            output_file.write('{sample}\t{well}\t{index}\n'.format(
+            output_file.write('{sample},{well},{index}\n'.format(
                 sample=sample.udf['Dx Fractienummer'],
                 well=well,
                 index=clarity_epp.export.utils.get_well_index(well, one_based=True)

From d87f019b48c2c07d1ae78df9f24ebaab917e561f Mon Sep 17 00:00:00 2001
From: Robert Ernst <r.f.ernst-3@umcutrecht.nl>
Date: Tue, 17 Jan 2023 15:34:30 +0100
Subject: [PATCH 28/41] Skip empty lines

---
 clarity_epp/upload/tecan.py | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/clarity_epp/upload/tecan.py b/clarity_epp/upload/tecan.py
index a10db71..509a616 100644
--- a/clarity_epp/upload/tecan.py
+++ b/clarity_epp/upload/tecan.py
@@ -123,11 +123,12 @@ def results_purify_normalise(lims, process_id):
             file_data = lims.get_file_contents(result_file.files[0].id).split('\n')
             header = file_data[0].rstrip().split(';')
             for line in file_data[1:]:
-                data = line.rstrip().split(';')
-                tecan_result[data[header.index('SampleID')]] = {
-                    'conc': float(data[header.index('Concentratie')]),
-                    'norm': txt_to_bool(data[header.index('Normalisatie')])
-                }
+                if line.rstrip():
+                    data = line.rstrip().split(';')
+                    tecan_result[data[header.index('SampleID')]] = {
+                        'conc': float(data[header.index('Concentratie')]),
+                        'norm': txt_to_bool(data[header.index('Normalisatie')])
+                    }
             break  # File found exit loop
 
     # Set concentration values on artifacts

From 763ce2d28b284360619e5bbf33e61b6e8ae09347 Mon Sep 17 00:00:00 2001
From: Robert Ernst <r.f.ernst-3@umcutrecht.nl>
Date: Tue, 17 Jan 2023 16:21:09 +0100
Subject: [PATCH 29/41] Change ',' to ';'

---
 clarity_epp/export/tecan.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/clarity_epp/export/tecan.py b/clarity_epp/export/tecan.py
index 1b61de0..2708dc7 100755
--- a/clarity_epp/export/tecan.py
+++ b/clarity_epp/export/tecan.py
@@ -30,11 +30,11 @@ def samplesheet(lims, process_id, type, output_file):
             ))
 
     elif type == 'purify_normalise':
-        output_file.write('SourceTubeID,PositionID,PositionIndex\n')
+        output_file.write('SourceTubeID;PositionID;PositionIndex\n')
         for well in clarity_epp.export.utils.sort_96_well_plate(well_plate.keys()):
             artifact = well_plate[well]
             sample = artifact.samples[0]  # assume one sample per tube
-            output_file.write('{sample},{well},{index}\n'.format(
+            output_file.write('{sample};{well};{index}\n'.format(
                 sample=sample.udf['Dx Fractienummer'],
                 well=well,
                 index=clarity_epp.export.utils.get_well_index(well, one_based=True)

From df9ad23bb09014c85f79ec92deb8da2d5d420322 Mon Sep 17 00:00:00 2001
From: Robert Ernst <r.f.ernst-3@umcutrecht.nl>
Date: Wed, 18 Jan 2023 13:23:31 +0100
Subject: [PATCH 30/41] Update header

---
 clarity_epp/upload/tecan.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/clarity_epp/upload/tecan.py b/clarity_epp/upload/tecan.py
index 509a616..20a4598 100644
--- a/clarity_epp/upload/tecan.py
+++ b/clarity_epp/upload/tecan.py
@@ -126,7 +126,7 @@ def results_purify_normalise(lims, process_id):
                 if line.rstrip():
                     data = line.rstrip().split(';')
                     tecan_result[data[header.index('SampleID')]] = {
-                        'conc': float(data[header.index('Concentratie')]),
+                        'conc': float(data[header.index('Concentratie(ng/ul)')]),
                         'norm': txt_to_bool(data[header.index('Normalisatie')])
                     }
             break  # File found exit loop

From 49df70cf9cd84e0025f7c4c352fa5a3403f8d470 Mon Sep 17 00:00:00 2001
From: Robert Ernst <r.f.ernst-3@umcutrecht.nl>
Date: Tue, 24 Jan 2023 17:37:51 +0100
Subject: [PATCH 31/41] Update workflow

---
 config.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/config.py b/config.py
index 8c40f48..14436aa 100755
--- a/config.py
+++ b/config.py
@@ -23,8 +23,8 @@
 stoftestcode_research = 'NGS_023'
 
 stoftestcode_workflow = {
-    stoftestcode_wes: '1106',  # DEV Dx smMIP Fingerprint v1.2
-    stoftestcode_mip: '1201',  # DEV Dx Exoom Magnis v1.0
+    stoftestcode_wes: '1654',  # DEV Dx Exoom Magnis v1.2
+    stoftestcode_mip: '1651',  # DEV Dx smMIP v1.2
 }
 
 # Export meetw protocol steps WES
@@ -75,7 +75,7 @@
 ]
 
 # Post sequencing workflow
-sequencing_workflow = '1301'  # DEV Dx Illumina Sequencing v1.0
+sequencing_workflow = '1653'  # DEV Dx Illumina Sequencing v1.1
 post_sequencing_workflow = '902'  # DEV Dx Bioinformatica analyses v1.0
 post_bioinf_workflow = {  # Contains workflow and workflow stage (number) for single or trio samples
     # WES : DEV Dx NGS WES onderzoeken afronden v1.1

From 6a2b00b04b3d8c0ca061456df2c244006b2826d0 Mon Sep 17 00:00:00 2001
From: Robert Ernst <r.f.ernst-3@umcutrecht.nl>
Date: Tue, 31 Jan 2023 15:59:08 +0100
Subject: [PATCH 32/41] Add support for tube output

---
 clarity_epp/export/manual_pipetting.py | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/clarity_epp/export/manual_pipetting.py b/clarity_epp/export/manual_pipetting.py
index d9a1346..c18f24d 100755
--- a/clarity_epp/export/manual_pipetting.py
+++ b/clarity_epp/export/manual_pipetting.py
@@ -398,7 +398,7 @@ def samplesheet_normalization(lims, process_id, output_file):
 
         # Save output under container location (well)
         well = ''.join(artifact.location[1].split(':'))
-        output[well] = (
+        output_data = (
             '{sample}\t{concentration:.1f}\t{sample_volume:.1f}\t{water_volume:.1f}\t'
             '{output:.1f}\t{evaporate}\t{container}\t{well}\n'
         ).format(
@@ -411,6 +411,10 @@ def samplesheet_normalization(lims, process_id, output_file):
             container=artifact.location[0].name,
             well=well
         )
+        if well == '11':  # Tube
+            output_file.write(output_data)
+        else:  # plate
+            output[well] = output_data
 
     for well in clarity_epp.export.utils.sort_96_well_plate(output.keys()):
         output_file.write(output[well])

From adbe48f90f1538b418c25a4b7f2c1c29c6af90b3 Mon Sep 17 00:00:00 2001
From: Robert Ernst <r.f.ernst-3@umcutrecht.nl>
Date: Tue, 14 Feb 2023 13:12:12 +0100
Subject: [PATCH 33/41] Only unpool complete sequencing runs.

---
 clarity_epp/placement/pool.py | 83 ++++++++++++++++++-----------------
 1 file changed, 42 insertions(+), 41 deletions(-)

diff --git a/clarity_epp/placement/pool.py b/clarity_epp/placement/pool.py
index de669a2..5f8b86a 100644
--- a/clarity_epp/placement/pool.py
+++ b/clarity_epp/placement/pool.py
@@ -9,44 +9,45 @@ def unpooling(lims, process_id):
     """Unpool samples after sequencing."""
     process = Process(lims, id=process_id)
 
-    pool_artifact = process.all_inputs()[0]
-    pool_artifact_parent_process = pool_artifact.parent_process
-    pool_artifact_demux = lims.get(pool_artifact.uri + '/demux')
-
-    run_id = pool_artifact.name  # Assume run id is set as pool name using placement/artifact/set_runid_name
-    sample_artifacts = []  # sample artifacts before pooling
-    sample_projects = {}
-
-    for artifact in pool_artifact_parent_process.result_files():
-        if (artifact.name == 'SampleSheet csv' or artifact.name == 'Sample Sheet') and artifact.files:
-            file_id = artifact.files[0].id
-            sample_sheet = lims.get_file_contents(id=file_id)
-            project_index = None
-            sample_index = None
-            for line in sample_sheet.split('\n'):
-                data = line.rstrip().split(',')
-
-                if 'Sample_Project' in data and 'Sample_ID' in data:
-                    project_index = data.index('Sample_Project')
-                    sample_index = data.index('Sample_ID')
-                elif project_index and len(data) >= project_index:
-                    sample_projects[data[sample_index]] = data[project_index]
-
-    for node in pool_artifact_demux.getiterator('artifact'):
-        if node.find('samples'):
-            if len(node.find('samples').findall('sample')) == 1:
-                sample_artifact = Artifact(lims, uri=node.attrib['uri'])
-                sample = sample_artifact.samples[0] # 1 sample per artifact.
-
-                # Get sample sequencing run and project from samplesheet
-                sample_artifact.udf['Dx Sequencing Run ID'] = run_id
-                if 'Sample Type' in sample.udf and 'library' in sample.udf['Sample Type']:  # Use sample.name for external (clarity_portal) samples
-                    sample_artifact.udf['Dx Sequencing Run Project'] = sample_projects[sample.name]
-                else:  # Use sample_artifact.name for Dx samples (upload via Helix)
-                    sample_artifact.udf['Dx Sequencing Run Project'] = sample_projects[sample_artifact.name]
-                sample_artifact.put()
-
-                if sample_artifact.samples[0].project and sample_artifact.samples[0].project.udf['Application'] == 'DX':  # Only move DX production samples to post sequencing workflow
-                    sample_artifacts.append(sample_artifact)
-
-    lims.route_artifacts(sample_artifacts, workflow_uri=Workflow(lims, id=config.post_sequencing_workflow).uri)
+    if process.step.actions.next_actions[0]['action'] == 'complete':  # Only unpool complete sequencing runs.
+        pool_artifact = process.all_inputs()[0]
+        pool_artifact_parent_process = pool_artifact.parent_process
+        pool_artifact_demux = lims.get(pool_artifact.uri + '/demux')
+
+        run_id = pool_artifact.name  # Assume run id is set as pool name using placement/artifact/set_runid_name
+        sample_artifacts = []  # sample artifacts before pooling
+        sample_projects = {}
+
+        for artifact in pool_artifact_parent_process.result_files():
+            if (artifact.name == 'SampleSheet csv' or artifact.name == 'Sample Sheet') and artifact.files:
+                file_id = artifact.files[0].id
+                sample_sheet = lims.get_file_contents(id=file_id)
+                project_index = None
+                sample_index = None
+                for line in sample_sheet.split('\n'):
+                    data = line.rstrip().split(',')
+
+                    if 'Sample_Project' in data and 'Sample_ID' in data:
+                        project_index = data.index('Sample_Project')
+                        sample_index = data.index('Sample_ID')
+                    elif project_index and len(data) >= project_index:
+                        sample_projects[data[sample_index]] = data[project_index]
+
+        for node in pool_artifact_demux.getiterator('artifact'):
+            if node.find('samples'):
+                if len(node.find('samples').findall('sample')) == 1:
+                    sample_artifact = Artifact(lims, uri=node.attrib['uri'])
+                    sample = sample_artifact.samples[0] # 1 sample per artifact.
+
+                    # Get sample sequencing run and project from samplesheet
+                    sample_artifact.udf['Dx Sequencing Run ID'] = run_id
+                    if 'Sample Type' in sample.udf and 'library' in sample.udf['Sample Type']:  # Use sample.name for external (clarity_portal) samples
+                        sample_artifact.udf['Dx Sequencing Run Project'] = sample_projects[sample.name]
+                    else:  # Use sample_artifact.name for Dx samples (upload via Helix)
+                        sample_artifact.udf['Dx Sequencing Run Project'] = sample_projects[sample_artifact.name]
+                    sample_artifact.put()
+
+                    if sample_artifact.samples[0].project and sample_artifact.samples[0].project.udf['Application'] == 'DX':  # Only move DX production samples to post sequencing workflow
+                        sample_artifacts.append(sample_artifact)
+
+        lims.route_artifacts(sample_artifacts, workflow_uri=Workflow(lims, id=config.post_sequencing_workflow).uri)

From 9c884c482a6f5499f5c3ffe8a2b90f9a70df0dcd Mon Sep 17 00:00:00 2001
From: Robert Ernst <r.f.ernst-3@umcutrecht.nl>
Date: Thu, 16 Feb 2023 12:38:17 +0100
Subject: [PATCH 34/41] Update workflow id

---
 config.py | 18 ++++++++++--------
 1 file changed, 10 insertions(+), 8 deletions(-)

diff --git a/config.py b/config.py
index 14436aa..c4428f7 100755
--- a/config.py
+++ b/config.py
@@ -1,19 +1,21 @@
 """Clarity epp configuration."""
 
 # Genologics
-baseuri = 'https://change_this_lims.uri'
-username = 'change_this'
-password = 'change_this'
+baseuri = 'https://usf-lims-test.op.umcutrecht.nl'
+# baseuri = 'https://usf-lims.umcutrecht.nl'
+username = 'DX_EPP'
+password = 'rVz2REm4tnu7'
 
 # Email settings
 email = {
-    'server': 'smtp.server.nl',
-    'from': 'from@email.nl',
+    'server': 'pim.umcutrecht.nl',
+    'from': 'r.f.ernst-3@umcutrecht.nl',
     'to_import_helix': [
-        'to_1@mail.nl',
+        'r.f.ernst-3@umcutrecht.nl',
+        'e.janson@umcutrecht.nl',
     ],
     'to_sequencing_run_complete': [
-        'to_1@mail.nl',
+        'r.f.ernst-3@umcutrecht.nl',
     ]
 }
 
@@ -75,7 +77,7 @@
 ]
 
 # Post sequencing workflow
-sequencing_workflow = '1653'  # DEV Dx Illumina Sequencing v1.1
+sequencing_workflow = '1701'  # DEV Dx Illumina Sequencing v1.2
 post_sequencing_workflow = '902'  # DEV Dx Bioinformatica analyses v1.0
 post_bioinf_workflow = {  # Contains workflow and workflow stage (number) for single or trio samples
     # WES : DEV Dx NGS WES onderzoeken afronden v1.1

From 9df9f5b52ff6dfc25145a6efa3bf63a2d9ec3865 Mon Sep 17 00:00:00 2001
From: Robert Ernst <r.f.ernst-3@umcutrecht.nl>
Date: Tue, 21 Feb 2023 10:54:23 +0100
Subject: [PATCH 35/41] Remove transform NoSpecialCharacters on sample name. Is
 managed on different location.

---
 .../NovaSeq_BCL2FASTQ_Reverse_Complement_Samplesheet.csv     | 5 +----
 templates/NovaSeq_BCL2FASTQ_Samplesheet.csv                  | 5 +----
 2 files changed, 2 insertions(+), 8 deletions(-)

diff --git a/templates/NovaSeq_BCL2FASTQ_Reverse_Complement_Samplesheet.csv b/templates/NovaSeq_BCL2FASTQ_Reverse_Complement_Samplesheet.csv
index cd08a8e..76622f2 100644
--- a/templates/NovaSeq_BCL2FASTQ_Reverse_Complement_Samplesheet.csv
+++ b/templates/NovaSeq_BCL2FASTQ_Reverse_Complement_Samplesheet.csv
@@ -29,7 +29,7 @@ Read2StartFromCycle,${PROCESS.UDF.UMI - Read 2 Start From Cycle}
 Sample_ID,Sample_Name,Sample_Plate,Sample_Well,index,index2,Sample_Project,Description
 </HEADER>
 <DATA>
-${INPUT.LIMSID},${SAMPLE.NAME##NoSpecialCharacters},${INPUT.CONTAINER.NAME},${INPUT.CONTAINER.PLACEMENT},${INPUT.REAGENT.SEQUENCE##Single},${INPUT.REAGENT.SEQUENCE##Index2RC},${SAMPLE.PROJECT.NAME##NoSpecialCharacters},
+${INPUT.LIMSID},${SAMPLE.NAME},${INPUT.CONTAINER.NAME},${INPUT.CONTAINER.PLACEMENT},${INPUT.REAGENT.SEQUENCE##Single},${INPUT.REAGENT.SEQUENCE##Index2RC},${SAMPLE.PROJECT.NAME##NoSpecialCharacters},
 </DATA>
 <TOKEN_FORMAT>
 ${INPUT.REAGENT.SEQUENCE##Single}
@@ -56,9 +56,6 @@ if (index > 0) {
     return ''
 }
 
-${SAMPLE.NAME##NoSpecialCharacters}
-return token.replaceAll(\"[^a-zA-Z0-9-]\", \"-\")
-
 ${SAMPLE.PROJECT.NAME##NoSpecialCharacters}
 return token.replaceAll(\"[^a-zA-Z0-9_]\", \"_\")
 
diff --git a/templates/NovaSeq_BCL2FASTQ_Samplesheet.csv b/templates/NovaSeq_BCL2FASTQ_Samplesheet.csv
index cc02f7f..7d9a6b2 100644
--- a/templates/NovaSeq_BCL2FASTQ_Samplesheet.csv
+++ b/templates/NovaSeq_BCL2FASTQ_Samplesheet.csv
@@ -30,7 +30,7 @@ Read2StartFromCycle,${PROCESS.UDF.UMI - Read 2 Start From Cycle}
 Sample_ID,Sample_Name,Sample_Plate,Sample_Well,index,index2,Sample_Project,Description
 </HEADER>
 <DATA>
-${INPUT.LIMSID},${SAMPLE.NAME##NoSpecialCharacters},${INPUT.CONTAINER.NAME},${INPUT.CONTAINER.PLACEMENT},${INPUT.REAGENT.SEQUENCE##Single},${INPUT.REAGENT.SEQUENCE##Dual},${SAMPLE.PROJECT.NAME##NoSpecialCharacters},
+${INPUT.LIMSID},${SAMPLE.NAME},${INPUT.CONTAINER.NAME},${INPUT.CONTAINER.PLACEMENT},${INPUT.REAGENT.SEQUENCE##Single},${INPUT.REAGENT.SEQUENCE##Dual},${SAMPLE.PROJECT.NAME##NoSpecialCharacters},
 </DATA>
 <TOKEN_FORMAT>
 ${INPUT.REAGENT.SEQUENCE##Single}
@@ -49,9 +49,6 @@ if (index >= 0) {
     return null
 }
 
-${SAMPLE.NAME##NoSpecialCharacters}
-return token.replaceAll(\"[^a-zA-Z0-9-]\", \"-\")
-
 ${SAMPLE.PROJECT.NAME##NoSpecialCharacters}
 return token.replaceAll(\"[^a-zA-Z0-9_]\", \"_\")
 

From 2ec058ab9995d6c6b65aef529fdc18e8288a067d Mon Sep 17 00:00:00 2001
From: Robert Ernst <r.f.ernst-3@umcutrecht.nl>
Date: Fri, 24 Feb 2023 10:50:06 +0100
Subject: [PATCH 36/41] Update config

---
 config.py | 16 +++++++---------
 1 file changed, 7 insertions(+), 9 deletions(-)

diff --git a/config.py b/config.py
index c4428f7..832b6a3 100755
--- a/config.py
+++ b/config.py
@@ -1,21 +1,19 @@
 """Clarity epp configuration."""
 
 # Genologics
-baseuri = 'https://usf-lims-test.op.umcutrecht.nl'
-# baseuri = 'https://usf-lims.umcutrecht.nl'
-username = 'DX_EPP'
-password = 'rVz2REm4tnu7'
+baseuri = 'https://change_this_lims.uri'
+username = 'change_this'
+password = 'change_this'
 
 # Email settings
 email = {
-    'server': 'pim.umcutrecht.nl',
-    'from': 'r.f.ernst-3@umcutrecht.nl',
+    'server': 'smtp.server.nl',
+    'from': 'from@email.nl',
     'to_import_helix': [
-        'r.f.ernst-3@umcutrecht.nl',
-        'e.janson@umcutrecht.nl',
+        'to_1@mail.nl',
     ],
     'to_sequencing_run_complete': [
-        'r.f.ernst-3@umcutrecht.nl',
+        'to_1@mail.nl',
     ]
 }
 

From 960912c6fdca1be89c359bb6ee77456d85f47d10 Mon Sep 17 00:00:00 2001
From: Robert Ernst <r.f.ernst-3@umcutrecht.nl>
Date: Fri, 24 Feb 2023 10:51:58 +0100
Subject: [PATCH 37/41] Update meetw config

---
 config.py | 12 +++++++++---
 1 file changed, 9 insertions(+), 3 deletions(-)

diff --git a/config.py b/config.py
index 832b6a3..9a0eda1 100755
--- a/config.py
+++ b/config.py
@@ -35,17 +35,23 @@
     'Dx Zuiveren gDNA manueel v1.1',
     'Dx manueel gezuiverd placement v1.2',
     'Dx gDNA Normalisatie Caliper v1.1',
-    'Dx Fragmenteren v1.0'
+    'Dx Uitvullen en zuiveren (Fluent 480) v1.0',
+    'Dx Normaliseren (Fluent 480) v1.0',
+    'Dx gDNA handmatige normalisatie WES v1.0'
 ]
 
-meetw_sampleprep_wes_processes = ['Dx Library Prep & Target Enrichment Magnis v1.0']
+meetw_sampleprep_wes_processes = [
+    'Dx Fragmenteren v1.0'
+    'Dx Library Prep & Target Enrichment Magnis v1.0'
+    ]
 
 meetw_seq_wes_processes = [
     'Dx Multiplexen Enrichment pools Magnis v1.0',
     'Dx Multiplexen sequence pool v1.2',
     'Dx Library pool denatureren en laden (NovaSeq) v1.3',
     'AUTOMATED - NovaSeq Run (NovaSeq 6000 v3.1)',
-    'Dx QC controle Lab sequencen v1.1'
+    'Dx QC controle Lab sequencen v1.1',
+    'Dx NovaSeq QC controle Lab sequencen v1.3'
 ]
 
 # Export meetw protocol steps MIP

From f9d51c87cf7445308618ce78679ad8ab7c2e3271 Mon Sep 17 00:00:00 2001
From: Robert Ernst <r.f.ernst-3@umcutrecht.nl>
Date: Fri, 24 Feb 2023 11:08:50 +0100
Subject: [PATCH 38/41] Fix python test?

---
 .github/workflows/python.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/python.yml b/.github/workflows/python.yml
index 227ceca..6f567d9 100644
--- a/.github/workflows/python.yml
+++ b/.github/workflows/python.yml
@@ -12,7 +12,7 @@ on:
 jobs:
   build:
 
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-20.04
     strategy:
       fail-fast: false
       matrix:

From 5a8b86f88904d17d849ba7425a85966b2ce3682b Mon Sep 17 00:00:00 2001
From: Robert Ernst <r.f.ernst-3@umcutrecht.nl>
Date: Fri, 24 Feb 2023 11:11:59 +0100
Subject: [PATCH 39/41] Fix python test?

---
 scripts/move_samples_to_new_workflow.py | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/scripts/move_samples_to_new_workflow.py b/scripts/move_samples_to_new_workflow.py
index f0e76e6..932d573 100644
--- a/scripts/move_samples_to_new_workflow.py
+++ b/scripts/move_samples_to_new_workflow.py
@@ -15,23 +15,23 @@
 skip_artifacts = ['']  # Add samples that should not be moved to new workflow
 
 artifacts = []
-print '# Old queue:', len(old_queue.artifacts)
+print('# Old queue:', len(old_queue.artifacts))
 
 for artifact in old_queue.artifacts:
     if artifact.name not in skip_artifacts:
-        print 'Move:', artifact.name
+        print('Move:', artifact.name)
         artifacts.append(artifact)
     else:
-        print 'Keep:', artifact.name
+        print('Keep:', artifact.name)
 
-print '# Move to new workflow:', len(artifacts)
+print('# Move to new workflow:', len(artifacts))
 
 # Move things to new workflow, uncomment to enable.
 # lims.route_artifacts(artifacts, stage_uri=old_stage.uri, unassign=True)  # remove from old stage
 # lims.route_artifacts(artifacts, workflow_uri=new_workflow.uri)  # add to new workflow
 
 old_queue = Queue(lims, id='')  # Example: Dx Sample registratie zuivering v1.0 = 1142 (same as step id)
-print '# Old queue:', len(old_queue.artifacts)
+print('# Old queue:', len(old_queue.artifacts))
 
 new_queue = Queue(lims, id='')  # Example: Dx Sample registratie zuivering v1.1 = 1342 (same as step id)
-print '# New queue:', len(new_queue.artifacts)
+print('# New queue:', len(new_queue.artifacts))

From 10ef657edd11826617f50509661187b5eaba7045 Mon Sep 17 00:00:00 2001
From: Robert Ernst <r.f.ernst-3@umcutrecht.nl>
Date: Wed, 8 Mar 2023 13:45:55 +0100
Subject: [PATCH 40/41] Add qc process concentration

---
 clarity_epp/export/manual_pipetting.py | 28 +++++++++++++++++++-------
 1 file changed, 21 insertions(+), 7 deletions(-)

diff --git a/clarity_epp/export/manual_pipetting.py b/clarity_epp/export/manual_pipetting.py
index c18f24d..a8e249d 100755
--- a/clarity_epp/export/manual_pipetting.py
+++ b/clarity_epp/export/manual_pipetting.py
@@ -10,24 +10,38 @@ def samplesheet_purify(lims, process_id, output_file):
     """Create manual pipetting samplesheet for purifying samples."""
     output_file.write('Fractienummer\tConcentration(ng/ul)\taantal ng te isoleren\tul gDNA\tul Water\n')
     process = Process(lims, id=process_id)
+    # Find all QC process types
+    qc_process_types = clarity_epp.export.utils.get_process_types(lims, ['Dx Qubit QC', 'Dx Tecan Spark 10M QC'])
 
     for container in process.output_containers():
         artifact = container.placements['1:1']  # asume tubes
         input_artifact = artifact.input_artifact_list()[0]  # asume one input artifact
         sample = artifact.samples[0]  # asume one sample per tube
 
+        # Find last qc process for artifact
+        qc_process = lims.get_processes(type=qc_process_types, inputartifactlimsid=input_artifact.id)
+        if qc_process:
+            qc_process = sorted(
+                lims.get_processes(type=qc_process_types, inputartifactlimsid=input_artifact.id),
+                key=lambda process: int(process.id.split('-')[-1])
+            )[-1]
+            for qc_artifact in qc_process.outputs_per_input(input_artifact.id):
+                if qc_artifact.name.split(' ')[0] == artifact.name:
+                    concentration = float(qc_artifact.udf['Dx Concentratie fluorescentie (ng/ul)'])
+
+        else:  # Fallback on previous process if qc process not found.
+            if 'Dx Concentratie fluorescentie (ng/ul)' in input_artifact.udf:
+                concentration = float(input_artifact.udf['Dx Concentratie fluorescentie (ng/ul)'])
+            elif 'Dx Concentratie OD (ng/ul)' in input_artifact.udf:
+                concentration = float(input_artifact.udf['Dx Concentratie OD (ng/ul)'])
+            elif 'Dx Concentratie (ng/ul)' in sample.udf:
+                concentration = float(sample.udf['Dx Concentratie (ng/ul)'])
+
         if 'Dx Fractienummer' in sample.udf:
             fractienummer = sample.udf['Dx Fractienummer']
         else:  # giab
             fractienummer = sample.name
 
-        if 'Dx Concentratie fluorescentie (ng/ul)' in input_artifact.udf:
-            concentration = float(input_artifact.udf['Dx Concentratie fluorescentie (ng/ul)'])
-        elif 'Dx Concentratie OD (ng/ul)' in input_artifact.udf:
-            concentration = float(input_artifact.udf['Dx Concentratie OD (ng/ul)'])
-        elif 'Dx Concentratie (ng/ul)' in sample.udf:
-            concentration = float(sample.udf['Dx Concentratie (ng/ul)'])
-
         input_gdna_ng = float(artifact.udf['Dx input hoeveelheid (ng)'])
         ul_gdna = input_gdna_ng/concentration
         ul_water = 200 - ul_gdna

From 8e84f3396d6a876cb0f18a80faed9dd6b04ff8e6 Mon Sep 17 00:00:00 2001
From: Robert Ernst <r.f.ernst-3@umcutrecht.nl>
Date: Thu, 16 Mar 2023 15:38:11 +0100
Subject: [PATCH 41/41] Fix config, add mising ','

---
 config.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/config.py b/config.py
index 9a0eda1..6e5a22a 100755
--- a/config.py
+++ b/config.py
@@ -41,7 +41,7 @@
 ]
 
 meetw_sampleprep_wes_processes = [
-    'Dx Fragmenteren v1.0'
+    'Dx Fragmenteren v1.0',
     'Dx Library Prep & Target Enrichment Magnis v1.0'
     ]