Merge branch 'develop' of https://github.com/sanger/limber into uat-2…

…023-oct-12

.release-version

@@ -1 +1 @@
-3.37.1
+3.38.0

app/models/labware_creators/pooled_wells_by_sample_in_groups.rb

@@ -12,12 +12,9 @@ module LabwareCreators
   class PooledWellsBySampleInGroups < Base
     include SupportParent::PlateOnly
 
-    # By default, source wells with the sample are pooled in pairs.
-    DEFAULT_NUMBER_OF_SOURCE_WELLS = 2
-
     # Number of source wells with the same sample to be pooled.
     def number_of_source_wells
-      purpose_config[:number_of_source_wells] || DEFAULT_NUMBER_OF_SOURCE_WELLS
+      @number_of_source_wells ||= purpose_config.dig(:creator_class, :args, :number_of_source_wells)
     end
 
     # Well filter with this object as the creator

config/mbrave.yml

@@ -1,5 +1,322 @@
 ---
 development: &1
+  Bioscan_forward_96_v3:
+    name: Bioscan_forward_96_v3
+    version: v3
+    num_plate: 1
+    tags:
+      - PB1F_bc1001
+      - PB1F_bc1002
+      - PB1F_bc1003
+      - PB1F_bc1004
+      - PB1F_bc1005
+      - PB1F_bc1006
+      - PB1F_bc1007
+      - PB1F_bc1008
+      - PB1F_bc1009
+      - PB1F_bc1010
+      - PB1F_bc1011
+      - PB1F_bc1012
+      - PB1F_bc1013
+      - PB1F_bc1014
+      - PB1F_bc1015
+      - PB1F_bc1016
+      - PB1F_bc1017
+      - PB1F_bc1018
+      - PB1F_bc1019
+      - PB1F_bc1020
+      - PB1F_bc1021
+      - PB1F_bc1022
+      - PB1F_bc1023
+      - PB1F_bc1024
+      - PB1F_bc1025
+      - PB1F_bc1026
+      - PB1F_bc1027
+      - PB1F_bc1028
+      - PB1F_bc1029
+      - PB1F_bc1030
+      - PB1F_bc1031
+      - PB1F_bc1032
+      - PB1F_bc1033
+      - PB1F_bc1034
+      - PB1F_bc1035
+      - PB1F_bc1036
+      - PB1F_bc1037
+      - PB1F_bc1038
+      - PB1F_bc1039
+      - PB1F_bc1040
+      - PB1F_bc1041
+      - PB1F_bc1042
+      - PB1F_bc1043
+      - PB1F_bc1044
+      - PB1F_bc1045
+      - PB1F_bc1046
+      - PB1F_bc1047
+      - PB1F_bc1048
+      - PB1F_bc1049
+      - PB1F_bc1050
+      - PB1F_bc1051
+      - PB1F_bc1052
+      - PB1F_bc1053
+      - PB1F_bc1054
+      - PB1F_bc1055
+      - PB1F_bc1056
+      - PB1F_bc1057
+      - PB1F_bc1058
+      - PB1F_bc1059
+      - PB1F_bc1060
+      - PB1F_bc1061
+      - PB1F_bc1062
+      - PB1F_bc1063
+      - PB1F_bc1064
+      - PB1F_bc1065
+      - PB1F_bc1066
+      - PB1F_bc1067
+      - PB1F_bc1068
+      - PB1F_bc1069
+      - PB1F_bc1195
+      - PB1F_bc1071
+      - PB1F_bc1072
+      - PB1F_bc1073
+      - PB1F_bc1074
+      - PB1F_bc1075
+      - PB1F_bc1076
+      - PB1F_bc1077
+      - PB1F_bc1078
+      - PB1F_bc1079
+      - PB1F_bc1080
+      - PB1F_bc1081
+      - PB1F_bc1082
+      - PB1F_bc1083
+      - PB1F_bc1084
+      - PB1F_bc1085
+      - PB1F_bc1086
+      - PB1F_bc1087
+      - PB1F_bc1088
+      - PB1F_bc1089
+      - PB1F_bc1090
+      - PB1F_bc1091
+      - PB1F_bc1092
+      - PB1F_bc1093
+      - PB1F_bc1094
+      - PB1F_bc1095
+      - PB1F_bc1096
+  Bioscan_reverse_4_1_v3:
+    name: Bioscan_reverse_4_1_v3
+    version: v3
+    num_plate: 1
+    tags:
+      - PB1R_bc1097_rc
+      - PB1R_bc1098_rc
+      - PB1R_bc1099_rc
+      - PB1R_bc1100_rc
+  Bioscan_reverse_4_2_v3:
+    name: Bioscan_reverse_4_2_v3
+    version: v3
+    num_plate: 2
+    tags:
+      - PB1R_bc1101_rc
+      - PB1R_bc1102_rc
+      - PB1R_bc1103_rc
+      - PB1R_bc1104_rc
+  Bioscan_reverse_4_3_v3:
+    name: Bioscan_reverse_4_3_v3
+    version: v3
+    num_plate: 3
+    tags:
+      - PB1R_bc1105_rc
+      - PB1R_bc1106_rc
+      - PB1R_bc1107_rc
+      - PB1R_bc1108_rc
+  Bioscan_reverse_4_4_v3:
+    name: Bioscan_reverse_4_4_v3
+    version: v3
+    num_plate: 4
+    tags:
+      - PB1R_bc1109_rc
+      - PB1R_bc1110_rc
+      - PB1R_bc1111_rc
+      - PB1R_bc1112_rc
+  Bioscan_reverse_4_5_v3:
+    name: Bioscan_reverse_4_5_v3
+    version: v3
+    num_plate: 5
+    tags:
+      - PB1R_bc1113_rc
+      - PB1R_bc1114_rc
+      - PB1R_bc1115_rc
+      - PB1R_bc1116_rc
+  Bioscan_reverse_4_6_v3:
+    name: Bioscan_reverse_4_6_v3
+    version: v3
+    num_plate: 6
+    tags:
+      - PB1R_bc1117_rc
+      - PB1R_bc1118_rc
+      - PB1R_bc1119_rc
+      - PB1R_bc1120_rc
+  Bioscan_reverse_4_7_v3:
+    name: Bioscan_reverse_4_7_v3
+    version: v3
+    num_plate: 7
+    tags:
+      - PB1R_bc1121_rc
+      - PB1R_bc1122_rc
+      - PB1R_bc1123_rc
+      - PB1R_bc1124_rc
+  Bioscan_reverse_4_8_v3:
+    name: Bioscan_reverse_4_8_v3
+    version: v3
+    num_plate: 8
+    tags:
+      - PB1R_bc1125_rc
+      - PB1R_bc1126_rc
+      - PB1R_bc1127_rc
+      - PB1R_bc1128_rc
+  Bioscan_reverse_4_9_v3:
+    name: Bioscan_reverse_4_9_v3
+    version: v3
+    num_plate: 9
+    tags:
+      - PB1R_bc1129_rc
+      - PB1R_bc1130_rc
+      - PB1R_bc1131_rc
+      - PB1R_bc1132_rc
+  Bioscan_reverse_4_10_v3:
+    name: Bioscan_reverse_4_10_v3
+    version: v3
+    num_plate: 10
+    tags:
+      - PB1R_bc1133_rc
+      - PB1R_bc1134_rc
+      - PB1R_bc1135_rc
+      - PB1R_bc1136_rc
+  Bioscan_reverse_4_11_v3:
+    name: Bioscan_reverse_4_11_v3
+    version: v3
+    num_plate: 11
+    tags:
+      - PB1R_bc1137_rc
+      - PB1R_bc1138_rc
+      - PB1R_bc1139_rc
+      - PB1R_bc1196_rc
+  Bioscan_reverse_4_12_v3:
+    name: Bioscan_reverse_4_12_v3
+    version: v3
+    num_plate: 12
+    tags:
+      - PB1R_bc1141_rc
+      - PB1R_bc1142_rc
+      - PB1R_bc1143_rc
+      - PB1R_bc1144_rc
+  Bioscan_reverse_4_13_v3:
+    name: Bioscan_reverse_4_13_v3
+    version: v3
+    num_plate: 13
+    tags:
+      - PB1R_bc1145_rc
+      - PB1R_bc1146_rc
+      - PB1R_bc1147_rc
+      - PB1R_bc1148_rc
+  Bioscan_reverse_4_14_v3:
+    name: Bioscan_reverse_4_14_v3
+    version: v3
+    num_plate: 14
+    tags:
+      - PB1R_bc1149_rc
+      - PB1R_bc1150_rc
+      - PB1R_bc1151_rc
+      - PB1R_bc1152_rc
+  Bioscan_reverse_4_15_v3:
+    name: Bioscan_reverse_4_15_v3
+    version: v3
+    num_plate: 15
+    tags:
+      - PB1R_bc1153_rc
+      - PB1R_bc1154_rc
+      - PB1R_bc1155_rc
+      - PB1R_bc1156_rc
+  Bioscan_reverse_4_16_v3:
+    name: Bioscan_reverse_4_16_v3
+    version: v3
+    num_plate: 16
+    tags:
+      - PB1R_bc1157_rc
+      - PB1R_bc1158_rc
+      - PB1R_bc1159_rc
+      - PB1R_bc1160_rc
+  Bioscan_reverse_4_17_v3:
+    name: Bioscan_reverse_4_17_v3
+    version: v3
+    num_plate: 17
+    tags:
+      - PB1R_bc1161_rc
+      - PB1R_bc1162_rc
+      - PB1R_bc1163_rc
+      - PB1R_bc1164_rc
+  Bioscan_reverse_4_18_v3:
+    name: Bioscan_reverse_4_18_v3
+    version: v3
+    num_plate: 18
+    tags:
+      - PB1R_bc1165_rc
+      - PB1R_bc1166_rc
+      - PB1R_bc1167_rc
+      - PB1R_bc1168_rc
+  Bioscan_reverse_4_19_v3:
+    name: Bioscan_reverse_4_19_v3
+    version: v3
+    num_plate: 19
+    tags:
+      - PB1R_bc1169_rc
+      - PB1R_bc1170_rc
+      - PB1R_bc1171_rc
+      - PB1R_bc1172_rc
+  Bioscan_reverse_4_20_v3:
+    name: Bioscan_reverse_4_20_v3
+    version: v3
+    num_plate: 20
+    tags:
+      - PB1R_bc1173_rc
+      - PB1R_bc1174_rc
+      - PB1R_bc1175_rc
+      - PB1R_bc1176_rc
+  Bioscan_reverse_4_21_v3:
+    name: Bioscan_reverse_4_21_v3
+    version: v3
+    num_plate: 21
+    tags:
+      - PB1R_bc1177_rc
+      - PB1R_bc1178_rc
+      - PB1R_bc1179_rc
+      - PB1R_bc1180_rc
+  Bioscan_reverse_4_22_v3:
+    name: Bioscan_reverse_4_22_v3
+    version: v3
+    num_plate: 22
+    tags:
+      - PB1R_bc1181_rc
+      - PB1R_bc1182_rc
+      - PB1R_bc1183_rc
+      - PB1R_bc1184_rc
+  Bioscan_reverse_4_23_v3:
+    name: Bioscan_reverse_4_23_v3
+    version: v3
+    num_plate: 23
+    tags:
+      - PB1R_bc1185_rc
+      - PB1R_bc1186_rc
+      - PB1R_bc1187_rc
+      - PB1R_bc1188_rc
+  Bioscan_reverse_4_24_v3:
+    name: Bioscan_reverse_4_24_v3
+    version: v3
+    num_plate: 24
+    tags:
+      - PB1R_bc1189_rc
+      - PB1R_bc1190_rc
+      - PB1R_bc1191_rc
+      - PB1R_bc1192_rc
   Bioscan_forward_96_v2:
     name: Bioscan_forward_96_v2
     version: v2

config/purposes/bioscan.yml

@@ -62,6 +62,30 @@ LBSN-384 PCR 2:
   # NB. will need to update this list to include new versions of the templates
   # as we generate new sets after changes from the scripts in Sequencescape
   :tag_layout_templates:
+    - Bioscan_384_template_1_v3
+    - Bioscan_384_template_2_v3
+    - Bioscan_384_template_3_v3
+    - Bioscan_384_template_4_v3
+    - Bioscan_384_template_5_v3
+    - Bioscan_384_template_6_v3
+    - Bioscan_384_template_7_v3
+    - Bioscan_384_template_8_v3
+    - Bioscan_384_template_9_v3
+    - Bioscan_384_template_10_v3
+    - Bioscan_384_template_11_v3
+    - Bioscan_384_template_12_v3
+    - Bioscan_384_template_13_v3
+    - Bioscan_384_template_14_v3
+    - Bioscan_384_template_15_v3
+    - Bioscan_384_template_16_v3
+    - Bioscan_384_template_17_v3
+    - Bioscan_384_template_18_v3
+    - Bioscan_384_template_19_v3
+    - Bioscan_384_template_20_v3
+    - Bioscan_384_template_21_v3
+    - Bioscan_384_template_22_v3
+    - Bioscan_384_template_23_v3
+    - Bioscan_384_template_24_v3
     - Bioscan_384_template_1_v2
     - Bioscan_384_template_2_v2
     - Bioscan_384_template_3_v2

config/purposes/scrna_core_cell_extraction.wip.yml

@@ -53,11 +53,13 @@ LRC Blood Bank:
 LRC PBMC Bank:
   :asset_type: plate
   # Labware creator for pooling isolations by sample before cell counting
-  :creator_class: LabwareCreators::PooledWellsBySampleInGroups
+  :creator_class:
+    name: LabwareCreators::PooledWellsBySampleInGroups
+    args:
+      # number of source wells to pool into a single destination well by sample from LRC Bank to LRC PBMC Bank
+      # e.g. 6 copies of sample in 6 wells, '2' in the config, pool to make 3 child wells
+      number_of_source_wells: 2
   :label_template: plate_cellaca_qc # creates QC1 up to QC4 barcodes
-  # number of source wells to pool into a single destination well by sample from LRC Bank to LRC PBMC Bank
-  # e.g. 6 copies of sample in 6 wells, '2' in the config, pool to make 3 child wells
-  :number_of_source_wells: 2
   :file_links:
     - name: 'Download Cellaca Input QC1'
       id: cellaca_input_file