@platforma-open/milaboratories.mixcr-clonotyping-2.workflow 3.1.1 → 3.2.1
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/.turbo/turbo-build.log +1 -1
- package/CHANGELOG.md +12 -0
- package/dist/tengo/lib/calculate-export-specs.lib.tengo +2 -3
- package/dist/tengo/lib/qc-report-columns.lib.tengo +277 -274
- package/dist/tengo/tpl/aggregate-by-clonotype-key.plj.gz +0 -0
- package/dist/tengo/tpl/calculate-preset-info.plj.gz +0 -0
- package/dist/tengo/tpl/export-report.plj.gz +0 -0
- package/dist/tengo/tpl/list-presets.plj.gz +0 -0
- package/dist/tengo/tpl/main.plj.gz +0 -0
- package/dist/tengo/tpl/mixcr-analyze.plj.gz +0 -0
- package/dist/tengo/tpl/mixcr-export.plj.gz +0 -0
- package/dist/tengo/tpl/prerun.plj.gz +0 -0
- package/dist/tengo/tpl/process-single-cell.plj.gz +0 -0
- package/dist/tengo/tpl/process.plj.gz +0 -0
- package/dist/tengo/tpl/test.columns-calculate.plj.gz +0 -0
- package/dist/tengo/tpl/test.columns.test.plj.gz +0 -0
- package/package.json +1 -1
- package/src/aggregate-by-clonotype-key.tpl.tengo +1 -1
- package/src/calculate-export-specs.lib.tengo +2 -3
- package/src/export-report.tpl.tengo +6 -3
- package/src/mixcr-export.tpl.tengo +17 -1
- package/src/process-single-cell.tpl.tengo +1 -1
- package/src/process.tpl.tengo +14 -5
- package/src/qc-report-columns.lib.tengo +277 -274
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@@ -5,7 +5,7 @@ ll := import("@platforma-sdk/workflow-tengo:ll")
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pConstants := import("@platforma-sdk/workflow-tengo:pframes.constants")
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// QC Report column specifications function
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getQcReportColumns := func(hasUmi, isSingleCell, sampleIdAxisSpec, chains) {
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getQcReportColumns := func(hasUmi, isSingleCell, sampleIdAxisSpec, chains, cellTags) {
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// Bulk sequencing columns
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baseColumns := [
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{
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@@ -489,7 +489,7 @@ getQcReportColumns := func(hasUmi, isSingleCell, sampleIdAxisSpec, chains) {
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column: "assemble.preCloneAssembler.unassignedAlignments",
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id: "assemble-pre-clone-assembler-unassigned-alignments",
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allowNA: true,
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naRegex: "",
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naRegex: "^[a-zA-Z_]*$",
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spec: {
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name: "mixcr.com/reports/assemble/preCloneAssembler/unassignedAlignments",
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valueType: "Long",
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@@ -505,7 +505,7 @@ getQcReportColumns := func(hasUmi, isSingleCell, sampleIdAxisSpec, chains) {
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column: "assemble.preCloneAssembler.unassignedAlignmentsPercents",
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id: "assemble-pre-clone-assembler-unassigned-alignments-percents",
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allowNA: true,
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naRegex: "",
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naRegex: "^[a-zA-Z_]*$",
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spec: {
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name: "mixcr.com/reports/assemble/preCloneAssembler/unassignedAlignmentsPercents",
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valueType: "Double",
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// Single Cell columns
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singleCellColumns := [
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},
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// {
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// column: "align.readsWithChain.IGH",
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// id: "align-reads-with-chain-igh",
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// allowNA: true,
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// naRegex: "",
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// spec: {
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// name: "mixcr.com/reports/align/readsWithChain/IGH",
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// valueType: "Long",
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// annotations: {
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// "pl7.app/min": "0",
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// "pl7.app/table/orderPriority": "96000",
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// "pl7.app/table/visibility": "optional",
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// "pl7.app/label": "Reads with Chain IGH"
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// }
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// }
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// },
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// {
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// column: "align.readsWithChain.IGHPercents",
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// id: "align-reads-with-chain-igh-percents",
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// allowNA: true,
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// name: "mixcr.com/reports/align/readsWithChain/IGHPercents",
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// valueType: "Double",
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// annotations: {
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// "pl7.app/table/visibility": "default",
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// "pl7.app/label": "Reads with Chain IGH (%)"
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// }
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// },
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// {
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// column: "align.readsWithChain.IGK",
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// id: "align-reads-with-chain-igk",
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// name: "mixcr.com/reports/align/readsWithChain/IGK",
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// annotations: {
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// "pl7.app/min": "0",
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// "pl7.app/table/orderPriority": "96200",
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// {
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// annotations: {
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// "pl7.app/min": "0",
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// }
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// },
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// {
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// column: "align.readsWithChain.IGL",
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// name: "mixcr.com/reports/align/readsWithChain/IGL",
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// annotations: {
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// "pl7.app/table/orderPriority": "96400",
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// }
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// },
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// }
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// },
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// {
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// allowNA: true,
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// annotations: {
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// "pl7.app/min": "0",
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// "pl7.app/table/orderPriority": "96700",
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// }
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// },
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// {
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// allowNA: true,
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// annotations: {
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// "pl7.app/min": "0",
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// "pl7.app/table/orderPriority": "96800",
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// "pl7.app/table/visibility": "default",
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// "pl7.app/label": "Reads with Chain TRAD (%)"
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// }
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// }
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|
+
// },
|
|
871
|
+
// {
|
|
872
|
+
// column: "align.readsWithChain.TRB",
|
|
873
|
+
// id: "align-reads-with-chain-trb",
|
|
874
|
+
// allowNA: true,
|
|
875
|
+
// naRegex: "",
|
|
876
|
+
// spec: {
|
|
877
|
+
// name: "mixcr.com/reports/align/readsWithChain/TRB",
|
|
878
|
+
// valueType: "Long",
|
|
879
|
+
// annotations: {
|
|
880
|
+
// "pl7.app/min": "0",
|
|
881
|
+
// "pl7.app/table/orderPriority": "97000",
|
|
882
|
+
// "pl7.app/table/visibility": "optional",
|
|
883
|
+
// "pl7.app/label": "Reads with Chain TRB"
|
|
884
|
+
// }
|
|
885
|
+
// }
|
|
886
|
+
// },
|
|
887
|
+
// {
|
|
888
|
+
// column: "align.readsWithChain.TRBPercents",
|
|
889
|
+
// id: "align-reads-with-chain-trb-percents",
|
|
890
|
+
// allowNA: true,
|
|
891
|
+
// naRegex: "",
|
|
892
|
+
// spec: {
|
|
893
|
+
// name: "mixcr.com/reports/align/readsWithChain/TRBPercents",
|
|
894
|
+
// valueType: "Double",
|
|
895
|
+
// annotations: {
|
|
896
|
+
// "pl7.app/min": "0",
|
|
897
|
+
// "pl7.app/max": "100",
|
|
898
|
+
// "pl7.app/table/orderPriority": "97100",
|
|
899
|
+
// "pl7.app/table/visibility": "default",
|
|
900
|
+
// "pl7.app/label": "Reads with Chain TRB (%)"
|
|
901
|
+
// }
|
|
902
|
+
// }
|
|
903
|
+
// },
|
|
904
|
+
// {
|
|
905
|
+
// column: "align.readsWithChain.TRG",
|
|
906
|
+
// id: "align-reads-with-chain-trg",
|
|
907
|
+
// allowNA: true,
|
|
908
|
+
// naRegex: "",
|
|
909
|
+
// spec: {
|
|
910
|
+
// name: "mixcr.com/reports/align/readsWithChain/TRG",
|
|
911
|
+
// valueType: "Long",
|
|
912
|
+
// annotations: {
|
|
913
|
+
// "pl7.app/min": "0",
|
|
914
|
+
// "pl7.app/table/orderPriority": "97200",
|
|
915
|
+
// "pl7.app/table/visibility": "optional",
|
|
916
|
+
// "pl7.app/label": "Reads with Chain TRG"
|
|
917
|
+
// }
|
|
918
|
+
// }
|
|
919
|
+
// },
|
|
920
|
+
// {
|
|
921
|
+
// column: "align.readsWithChain.TRGPercents",
|
|
922
|
+
// id: "align-reads-with-chain-trg-percents",
|
|
923
|
+
// allowNA: true,
|
|
924
|
+
// naRegex: "",
|
|
925
|
+
// spec: {
|
|
926
|
+
// name: "mixcr.com/reports/align/readsWithChain/TRGPercents",
|
|
927
|
+
// valueType: "Double",
|
|
928
|
+
// annotations: {
|
|
929
|
+
// "pl7.app/min": "0",
|
|
930
|
+
// "pl7.app/max": "100",
|
|
931
|
+
// "pl7.app/table/orderPriority": "97300",
|
|
932
|
+
// "pl7.app/table/visibility": "default",
|
|
933
|
+
// "pl7.app/label": "Reads with Chain TRG (%)"
|
|
934
|
+
// }
|
|
935
|
+
// }
|
|
936
|
+
// },
|
|
937
937
|
{
|
|
938
938
|
column: "assembleCells.cellBarcodesWithFoundGroups",
|
|
939
939
|
id: "assemble-cells-cell-barcodes-with-found-groups",
|
|
@@ -1180,93 +1180,96 @@ getQcReportColumns := func(hasUmi, isSingleCell, sampleIdAxisSpec, chains) {
|
|
|
1180
1180
|
"pl7.app/label": "Unassigned Clonotypes (%)"
|
|
1181
1181
|
}
|
|
1182
1182
|
}
|
|
1183
|
-
},
|
|
1184
|
-
{
|
|
1185
|
-
column: "refineTags.CELL.outputCount",
|
|
1186
|
-
id: "refine-tags-cell-output-count",
|
|
1187
|
-
allowNA: true,
|
|
1188
|
-
naRegex: "NaN",
|
|
1189
|
-
spec: {
|
|
1190
|
-
name: "mixcr.com/reports/refineTags/CELL/outputCount",
|
|
1191
|
-
valueType: "Long",
|
|
1192
|
-
annotations: {
|
|
1193
|
-
"pl7.app/min": "0",
|
|
1194
|
-
"pl7.app/table/orderPriority": "85800",
|
|
1195
|
-
"pl7.app/table/visibility": "optional",
|
|
1196
|
-
"pl7.app/label": "Refine Tags CELL - Output Count"
|
|
1197
|
-
}
|
|
1198
|
-
}
|
|
1199
|
-
},
|
|
1200
|
-
{
|
|
1201
|
-
column: "refineTags.CELL.outputCountPercents",
|
|
1202
|
-
id: "refine-tags-cell-output-count-percents",
|
|
1203
|
-
allowNA: true,
|
|
1204
|
-
naRegex: "NaN",
|
|
1205
|
-
spec: {
|
|
1206
|
-
name: "mixcr.com/reports/refineTags/CELL/outputCountPercents",
|
|
1207
|
-
valueType: "Double",
|
|
1208
|
-
annotations: {
|
|
1209
|
-
"pl7.app/min": "0",
|
|
1210
|
-
"pl7.app/max": "100",
|
|
1211
|
-
"pl7.app/table/orderPriority": "85900",
|
|
1212
|
-
"pl7.app/table/visibility": "default",
|
|
1213
|
-
"pl7.app/label": "Refine Tags CELL - Output Count (%)"
|
|
1214
|
-
}
|
|
1215
|
-
}
|
|
1216
|
-
},
|
|
1217
|
-
{
|
|
1218
|
-
column: "refineTags.CELL.outputDiversity",
|
|
1219
|
-
id: "refine-tags-cell-output-diversity",
|
|
1220
|
-
allowNA: true,
|
|
1221
|
-
naRegex: "NaN",
|
|
1222
|
-
spec: {
|
|
1223
|
-
name: "mixcr.com/reports/refineTags/CELL/outputDiversity",
|
|
1224
|
-
valueType: "Long",
|
|
1225
|
-
annotations: {
|
|
1226
|
-
"pl7.app/min": "0",
|
|
1227
|
-
"pl7.app/table/orderPriority": "86000",
|
|
1228
|
-
"pl7.app/table/visibility": "optional",
|
|
1229
|
-
"pl7.app/label": "Refine Tags CELL - Output Diversity"
|
|
1230
|
-
}
|
|
1231
|
-
}
|
|
1232
|
-
},
|
|
1233
|
-
{
|
|
1234
|
-
column: "refineTags.CELL.outputDiversityPercents",
|
|
1235
|
-
id: "refine-tags-cell-output-diversity-percents",
|
|
1236
|
-
allowNA: true,
|
|
1237
|
-
naRegex: "NaN",
|
|
1238
|
-
spec: {
|
|
1239
|
-
name: "mixcr.com/reports/refineTags/CELL/outputDiversityPercents",
|
|
1240
|
-
valueType: "Double",
|
|
1241
|
-
annotations: {
|
|
1242
|
-
"pl7.app/min": "0",
|
|
1243
|
-
"pl7.app/max": "100",
|
|
1244
|
-
"pl7.app/table/orderPriority": "86100",
|
|
1245
|
-
"pl7.app/table/visibility": "default",
|
|
1246
|
-
"pl7.app/label": "Refine Tags CELL - Output Diversity (%)"
|
|
1247
|
-
}
|
|
1248
|
-
}
|
|
1249
1183
|
}]
|
|
1250
1184
|
|
|
1251
|
-
for
|
|
1185
|
+
for cellTag in cellTags {
|
|
1252
1186
|
singleCellColumns += [{
|
|
1253
|
-
column: "
|
|
1254
|
-
id: "
|
|
1187
|
+
column: "refineTags." + cellTag + ".outputCount",
|
|
1188
|
+
id: "refine-tags-" + cellTag + "-output-count",
|
|
1255
1189
|
allowNA: true,
|
|
1256
|
-
naRegex: "",
|
|
1190
|
+
naRegex: "NaN",
|
|
1257
1191
|
spec: {
|
|
1258
|
-
name: "mixcr.com/reports/
|
|
1192
|
+
name: "mixcr.com/reports/refineTags/CELL/outputCount",
|
|
1259
1193
|
valueType: "Long",
|
|
1260
1194
|
annotations: {
|
|
1261
1195
|
"pl7.app/min": "0",
|
|
1262
|
-
"pl7.app/table/orderPriority": "
|
|
1196
|
+
"pl7.app/table/orderPriority": "85800",
|
|
1263
1197
|
"pl7.app/table/visibility": "optional",
|
|
1264
|
-
"pl7.app/label": "
|
|
1198
|
+
"pl7.app/label": "Refine Tags " + cellTag + " - Output Count"
|
|
1199
|
+
}
|
|
1200
|
+
}
|
|
1201
|
+
},
|
|
1202
|
+
{
|
|
1203
|
+
column: "refineTags." + cellTag + ".outputCountPercents",
|
|
1204
|
+
id: "refine-tags-" + cellTag + "-output-count-percents",
|
|
1205
|
+
allowNA: true,
|
|
1206
|
+
naRegex: "NaN",
|
|
1207
|
+
spec: {
|
|
1208
|
+
name: "mixcr.com/reports/refineTags/CELL/outputCountPercents",
|
|
1209
|
+
valueType: "Double",
|
|
1210
|
+
annotations: {
|
|
1211
|
+
"pl7.app/min": "0",
|
|
1212
|
+
"pl7.app/max": "100",
|
|
1213
|
+
"pl7.app/table/orderPriority": "85900",
|
|
1214
|
+
"pl7.app/table/visibility": "default",
|
|
1215
|
+
"pl7.app/label": "Refine Tags " + cellTag + " - Output Count (%)"
|
|
1216
|
+
}
|
|
1217
|
+
}
|
|
1218
|
+
},
|
|
1219
|
+
{
|
|
1220
|
+
column: "refineTags." + cellTag + ".outputDiversity",
|
|
1221
|
+
id: "refine-tags-" + cellTag + "-output-diversity",
|
|
1222
|
+
allowNA: true,
|
|
1223
|
+
naRegex: "NaN",
|
|
1224
|
+
spec: {
|
|
1225
|
+
name: "mixcr.com/reports/refineTags/CELL/outputDiversity",
|
|
1226
|
+
valueType: "Long",
|
|
1227
|
+
annotations: {
|
|
1228
|
+
"pl7.app/min": "0",
|
|
1229
|
+
"pl7.app/table/orderPriority": "86000",
|
|
1230
|
+
"pl7.app/table/visibility": "optional",
|
|
1231
|
+
"pl7.app/label": "Refine Tags " + cellTag + " - Output Diversity"
|
|
1232
|
+
}
|
|
1233
|
+
}
|
|
1234
|
+
},
|
|
1235
|
+
{
|
|
1236
|
+
column: "refineTags." + cellTag + ".outputDiversityPercents",
|
|
1237
|
+
id: "refine-tags-" + cellTag + "-output-diversity-percents",
|
|
1238
|
+
allowNA: true,
|
|
1239
|
+
naRegex: "NaN",
|
|
1240
|
+
spec: {
|
|
1241
|
+
name: "mixcr.com/reports/refineTags/CELL/outputDiversityPercents",
|
|
1242
|
+
valueType: "Double",
|
|
1243
|
+
annotations: {
|
|
1244
|
+
"pl7.app/min": "0",
|
|
1245
|
+
"pl7.app/max": "100",
|
|
1246
|
+
"pl7.app/table/orderPriority": "86100",
|
|
1247
|
+
"pl7.app/table/visibility": "default",
|
|
1248
|
+
"pl7.app/label": "Refine Tags " + cellTag + " - Output Diversity (%)"
|
|
1265
1249
|
}
|
|
1266
1250
|
}
|
|
1267
1251
|
}]
|
|
1268
1252
|
}
|
|
1269
1253
|
|
|
1254
|
+
// for chain in chains {
|
|
1255
|
+
// singleCellColumns += [{
|
|
1256
|
+
// column: "clonesWithChain." + chain,
|
|
1257
|
+
// id: "clones-with-chain-" + chain,
|
|
1258
|
+
// allowNA: true,
|
|
1259
|
+
// naRegex: "",
|
|
1260
|
+
// spec: {
|
|
1261
|
+
// name: "mixcr.com/reports/clonesWithChain/" + chain,
|
|
1262
|
+
// valueType: "Long",
|
|
1263
|
+
// annotations: {
|
|
1264
|
+
// "pl7.app/min": "0",
|
|
1265
|
+
// "pl7.app/table/orderPriority": "97400",
|
|
1266
|
+
// "pl7.app/table/visibility": "optional",
|
|
1267
|
+
// "pl7.app/label": "Clones with Chain " + chain
|
|
1268
|
+
// }
|
|
1269
|
+
// }
|
|
1270
|
+
// }]
|
|
1271
|
+
// }
|
|
1272
|
+
|
|
1270
1273
|
columns := baseColumns
|
|
1271
1274
|
if hasUmi {
|
|
1272
1275
|
columns = columns + dataWithUmiColumns
|