@platforma-open/milaboratories.mixcr-clonotyping-2.workflow 3.22.0 → 3.23.1
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 +4 -2
- package/CHANGELOG.md +12 -0
- package/dist/tengo/lib/calculate-export-specs.lib.tengo +18 -0
- package/dist/tengo/lib/qc-report-columns.lib.tengo +238 -233
- package/dist/tengo/lib/stop-codon-replacement.lib.tengo +179 -0
- 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 +6 -6
- package/src/calculate-export-specs.lib.tengo +18 -0
- package/src/calculate-preset-info.tpl.tengo +2 -0
- package/src/export-report.tpl.tengo +98 -6
- package/src/list-presets.tpl.tengo +1 -0
- package/src/main.tpl.tengo +3 -1
- package/src/mixcr-analyze.tpl.tengo +1 -0
- package/src/mixcr-export.tpl.tengo +40 -1
- package/src/process.tpl.tengo +14 -1
- package/src/qc-report-columns.lib.tengo +238 -233
- package/src/stop-codon-replacement.lib.tengo +179 -0
package/.turbo/turbo-build.log
CHANGED
|
@@ -1,7 +1,7 @@
|
|
|
1
1
|
WARN Issue while reading "/home/runner/work/mixcr-clonotyping/mixcr-clonotyping/.npmrc". Failed to replace env in config: ${NPMJS_TOKEN}
|
|
2
2
|
|
|
3
|
-
> @platforma-open/milaboratories.mixcr-clonotyping-2.workflow@3.
|
|
4
|
-
> rm -rf dist && pl-tengo check && pl-tengo build
|
|
3
|
+
> @platforma-open/milaboratories.mixcr-clonotyping-2.workflow@3.23.1 build /home/runner/work/mixcr-clonotyping/mixcr-clonotyping/workflow
|
|
4
|
+
> shx rm -rf dist && pl-tengo check && pl-tengo build
|
|
5
5
|
|
|
6
6
|
info: Skipping unknown file type: test/columns.test.ts
|
|
7
7
|
Processing "src/aggregate-by-clonotype-key.tpl.tengo"...
|
|
@@ -17,6 +17,7 @@ Processing "src/prerun.tpl.tengo"...
|
|
|
17
17
|
Processing "src/process-single-cell.tpl.tengo"...
|
|
18
18
|
Processing "src/process.tpl.tengo"...
|
|
19
19
|
Processing "src/qc-report-columns.lib.tengo"...
|
|
20
|
+
Processing "src/stop-codon-replacement.lib.tengo"...
|
|
20
21
|
Processing "src/test/columns-calculate.tpl.tengo"...
|
|
21
22
|
Processing "src/test/columns.test.tpl.tengo"...
|
|
22
23
|
No syntax errors found.
|
|
@@ -25,6 +26,7 @@ No syntax errors found.
|
|
|
25
26
|
info: - writing /home/runner/work/mixcr-clonotyping/mixcr-clonotyping/workflow/dist/tengo/lib/calculate-export-specs.lib.tengo
|
|
26
27
|
info: - writing /home/runner/work/mixcr-clonotyping/mixcr-clonotyping/workflow/dist/tengo/lib/clonotype-label.lib.tengo
|
|
27
28
|
info: - writing /home/runner/work/mixcr-clonotyping/mixcr-clonotyping/workflow/dist/tengo/lib/qc-report-columns.lib.tengo
|
|
29
|
+
info: - writing /home/runner/work/mixcr-clonotyping/mixcr-clonotyping/workflow/dist/tengo/lib/stop-codon-replacement.lib.tengo
|
|
28
30
|
info: - writing /home/runner/work/mixcr-clonotyping/mixcr-clonotyping/workflow/dist/tengo/tpl/aggregate-by-clonotype-key.plj.gz
|
|
29
31
|
info: - writing /home/runner/work/mixcr-clonotyping/mixcr-clonotyping/workflow/dist/tengo/tpl/calculate-preset-info.plj.gz
|
|
30
32
|
info: - writing /home/runner/work/mixcr-clonotyping/mixcr-clonotyping/workflow/dist/tengo/tpl/export-report.plj.gz
|
package/CHANGELOG.md
CHANGED
|
@@ -1,5 +1,17 @@
|
|
|
1
1
|
# @platforma-open/milaboratories.mixcr-clonotyping.workflow
|
|
2
2
|
|
|
3
|
+
## 3.23.1
|
|
4
|
+
|
|
5
|
+
### Patch Changes
|
|
6
|
+
|
|
7
|
+
- 6f30f09: Upgrade MiXCR to 4.7.0-300-develop, add MI_LICENSE_DEBUG env, fix assembleCells column error in SC QC report, show loading spinner while sample list loads
|
|
8
|
+
|
|
9
|
+
## 3.23.0
|
|
10
|
+
|
|
11
|
+
### Minor Changes
|
|
12
|
+
|
|
13
|
+
- 3c8ed71: stop codon replacement and dep updates
|
|
14
|
+
|
|
3
15
|
## 3.22.0
|
|
4
16
|
|
|
5
17
|
### Minor Changes
|
|
@@ -442,6 +442,9 @@ calculateExportSpecs := func(presetSpecForBack, sampleIdAxisSpec, blockId, expor
|
|
|
442
442
|
}
|
|
443
443
|
|
|
444
444
|
orderP := 80000
|
|
445
|
+
aminoAcidSeqColumns := []
|
|
446
|
+
aminoAcidSeqColumnPairs := []
|
|
447
|
+
cdr3SeqColumns := []
|
|
445
448
|
|
|
446
449
|
|
|
447
450
|
|
|
@@ -466,6 +469,16 @@ calculateExportSpecs := func(presetSpecForBack, sampleIdAxisSpec, blockId, expor
|
|
|
466
469
|
alphabetShortMixcr := isAminoAcid ? "aa" : "n"
|
|
467
470
|
columnName := alphabetShortMixcr + "Seq" + imputedU + featureInFrameU
|
|
468
471
|
visibility := featureU == "CDR3" && (!isSingleCell || isAminoAcid) // isSingleCell ? (featureU == "CDR3") && isAminoAcid : (featureU == "CDR3") || (featureU == assemblingFeature)
|
|
472
|
+
if featureU == "CDR3" {
|
|
473
|
+
cdr3SeqColumns += [ columnName ]
|
|
474
|
+
}
|
|
475
|
+
if isAminoAcid {
|
|
476
|
+
aminoAcidSeqColumns += [ columnName ]
|
|
477
|
+
aminoAcidSeqColumnPairs += [ {
|
|
478
|
+
aa: columnName,
|
|
479
|
+
nt: "nSeq" + imputedU + featureU
|
|
480
|
+
} ]
|
|
481
|
+
}
|
|
469
482
|
columnsSpecPerClonotypeNoAggregates += [ {
|
|
470
483
|
column: columnName,
|
|
471
484
|
id: alphabetShortMixcr + "-seq-" + featureInFrameL + (isImputed ? "-imputed" : ""),
|
|
@@ -973,6 +986,7 @@ calculateExportSpecs := func(presetSpecForBack, sampleIdAxisSpec, blockId, expor
|
|
|
973
986
|
}
|
|
974
987
|
|
|
975
988
|
return {
|
|
989
|
+
productiveFeature: productiveFeature,
|
|
976
990
|
clonotypeKeyColumns: clonotypeKeyColumns,
|
|
977
991
|
clonotypeKeyArgs: clonotypeKeyArgs,
|
|
978
992
|
|
|
@@ -981,6 +995,10 @@ calculateExportSpecs := func(presetSpecForBack, sampleIdAxisSpec, blockId, expor
|
|
|
981
995
|
axisByClonotypeKeyGen: axisByClonotypeKeyGen,
|
|
982
996
|
axisByScClonotypeKeyGen: axisByScClonotypeKeyGen,
|
|
983
997
|
|
|
998
|
+
aminoAcidSeqColumns: aminoAcidSeqColumns,
|
|
999
|
+
aminoAcidSeqColumnPairs: aminoAcidSeqColumnPairs,
|
|
1000
|
+
cdr3SeqColumns: cdr3SeqColumns,
|
|
1001
|
+
|
|
984
1002
|
columnsSpecPerSample: columnsSpecPerSample,
|
|
985
1003
|
columnsSpecPerSampleSc: columnsSpecPerSampleSc,
|
|
986
1004
|
columnsSpecPerClonotypeNoAggregates: columnsSpecPerClonotypeNoAggregates,
|
|
@@ -6,7 +6,7 @@ pConstants := import("@platforma-sdk/workflow-tengo:pframes.constants")
|
|
|
6
6
|
text := import("text")
|
|
7
7
|
|
|
8
8
|
|
|
9
|
-
getQcReportColumns := func(hasUmi, isSingleCell, sampleIdAxisSpec, chains, cellTags, umiTags) {
|
|
9
|
+
getQcReportColumns := func(hasUmi, isSingleCell, sampleIdAxisSpec, chains, cellTags, umiTags, hasAssembleCells) {
|
|
10
10
|
if is_undefined(umiTags) {
|
|
11
11
|
umiTags = []
|
|
12
12
|
}
|
|
@@ -1045,253 +1045,258 @@ getQcReportColumns := func(hasUmi, isSingleCell, sampleIdAxisSpec, chains, cellT
|
|
|
1045
1045
|
|
|
1046
1046
|
|
|
1047
1047
|
|
|
1048
|
-
|
|
1049
|
-
|
|
1050
|
-
|
|
1051
|
-
|
|
1052
|
-
|
|
1053
|
-
|
|
1054
|
-
|
|
1055
|
-
|
|
1056
|
-
|
|
1057
|
-
|
|
1058
|
-
"
|
|
1059
|
-
|
|
1060
|
-
|
|
1048
|
+
]
|
|
1049
|
+
|
|
1050
|
+
if hasAssembleCells {
|
|
1051
|
+
singleCellColumns += [
|
|
1052
|
+
{
|
|
1053
|
+
column: "assembleCells.cellBarcodesWithFoundGroups",
|
|
1054
|
+
id: "assemble-cells-cell-barcodes-with-found-groups",
|
|
1055
|
+
allowNA: true,
|
|
1056
|
+
naRegex: "NaN",
|
|
1057
|
+
spec: {
|
|
1058
|
+
name: "mixcr.com/reports/assembleCells/cellBarcodesWithFoundGroups",
|
|
1059
|
+
valueType: "Long",
|
|
1060
|
+
annotations: {
|
|
1061
|
+
"pl7.app/min": "0",
|
|
1062
|
+
"pl7.app/table/orderPriority": "65000",
|
|
1063
|
+
"pl7.app/table/visibility": "optional",
|
|
1064
|
+
"pl7.app/label": "Cell Barcodes with Found Groups"
|
|
1065
|
+
}
|
|
1061
1066
|
}
|
|
1062
|
-
}
|
|
1063
|
-
|
|
1064
|
-
|
|
1065
|
-
|
|
1066
|
-
|
|
1067
|
-
|
|
1068
|
-
|
|
1069
|
-
|
|
1070
|
-
|
|
1071
|
-
|
|
1072
|
-
|
|
1073
|
-
|
|
1074
|
-
|
|
1075
|
-
|
|
1076
|
-
|
|
1077
|
-
|
|
1067
|
+
},
|
|
1068
|
+
{
|
|
1069
|
+
column: "assembleCells.cellBarcodesWithFoundGroupsPercents",
|
|
1070
|
+
id: "assemble-cells-cell-barcodes-with-found-groups-percents",
|
|
1071
|
+
allowNA: true,
|
|
1072
|
+
naRegex: "NaN",
|
|
1073
|
+
spec: {
|
|
1074
|
+
name: "mixcr.com/reports/assembleCells/cellBarcodesWithFoundGroupsPercents",
|
|
1075
|
+
valueType: "Double",
|
|
1076
|
+
annotations: {
|
|
1077
|
+
"pl7.app/min": "0",
|
|
1078
|
+
"pl7.app/max": "100",
|
|
1079
|
+
"pl7.app/table/orderPriority": "64100",
|
|
1080
|
+
"pl7.app/table/visibility": "default",
|
|
1081
|
+
"pl7.app/label": "Cell Barcodes with Found Groups (%)"
|
|
1082
|
+
}
|
|
1078
1083
|
}
|
|
1079
|
-
}
|
|
1080
|
-
|
|
1081
|
-
|
|
1082
|
-
|
|
1083
|
-
|
|
1084
|
-
|
|
1085
|
-
|
|
1086
|
-
|
|
1087
|
-
|
|
1088
|
-
|
|
1089
|
-
|
|
1090
|
-
|
|
1091
|
-
|
|
1092
|
-
|
|
1093
|
-
|
|
1084
|
+
},
|
|
1085
|
+
{
|
|
1086
|
+
column: "assembleCells.cellsNotIncludedBecauseContamination",
|
|
1087
|
+
id: "assemble-cells-cells-not-included-because-contamination",
|
|
1088
|
+
allowNA: true,
|
|
1089
|
+
naRegex: "",
|
|
1090
|
+
spec: {
|
|
1091
|
+
name: "mixcr.com/reports/assembleCells/cellsNotIncludedBecauseContamination",
|
|
1092
|
+
valueType: "Long",
|
|
1093
|
+
annotations: {
|
|
1094
|
+
"pl7.app/min": "0",
|
|
1095
|
+
"pl7.app/table/orderPriority": "64200",
|
|
1096
|
+
"pl7.app/table/visibility": "optional",
|
|
1097
|
+
"pl7.app/label": "Cells Not Included Because Contamination"
|
|
1098
|
+
}
|
|
1094
1099
|
}
|
|
1095
|
-
}
|
|
1096
|
-
|
|
1097
|
-
|
|
1098
|
-
|
|
1099
|
-
|
|
1100
|
-
|
|
1101
|
-
|
|
1102
|
-
|
|
1103
|
-
|
|
1104
|
-
|
|
1105
|
-
|
|
1106
|
-
|
|
1107
|
-
|
|
1108
|
-
|
|
1109
|
-
|
|
1110
|
-
|
|
1100
|
+
},
|
|
1101
|
+
{
|
|
1102
|
+
column: "assembleCells.cellsNotIncludedBecauseContaminationPercents",
|
|
1103
|
+
id: "assemble-cells-cells-not-included-because-contamination-percents",
|
|
1104
|
+
allowNA: true,
|
|
1105
|
+
naRegex: "NaN",
|
|
1106
|
+
spec: {
|
|
1107
|
+
name: "mixcr.com/reports/assembleCells/cellsNotIncludedBecauseContaminationPercents",
|
|
1108
|
+
valueType: "Double",
|
|
1109
|
+
annotations: {
|
|
1110
|
+
"pl7.app/min": "0",
|
|
1111
|
+
"pl7.app/max": "100",
|
|
1112
|
+
"pl7.app/table/orderPriority": "64300",
|
|
1113
|
+
"pl7.app/table/visibility": "default",
|
|
1114
|
+
"pl7.app/label": "Cells Not Included Because Contamination (%)"
|
|
1115
|
+
}
|
|
1111
1116
|
}
|
|
1112
|
-
}
|
|
1113
|
-
|
|
1114
|
-
|
|
1115
|
-
|
|
1116
|
-
|
|
1117
|
-
|
|
1118
|
-
|
|
1119
|
-
|
|
1120
|
-
|
|
1121
|
-
|
|
1122
|
-
|
|
1123
|
-
|
|
1124
|
-
|
|
1125
|
-
|
|
1126
|
-
|
|
1117
|
+
},
|
|
1118
|
+
{
|
|
1119
|
+
column: "assembleCells.cloneContamination",
|
|
1120
|
+
id: "assemble-cells-clone-contamination",
|
|
1121
|
+
allowNA: true,
|
|
1122
|
+
naRegex: "NaN",
|
|
1123
|
+
spec: {
|
|
1124
|
+
name: "mixcr.com/reports/assembleCells/cloneContamination",
|
|
1125
|
+
valueType: "Long",
|
|
1126
|
+
annotations: {
|
|
1127
|
+
"pl7.app/min": "0",
|
|
1128
|
+
"pl7.app/table/orderPriority": "64400",
|
|
1129
|
+
"pl7.app/table/visibility": "optional",
|
|
1130
|
+
"pl7.app/label": "Clone Contamination"
|
|
1131
|
+
}
|
|
1127
1132
|
}
|
|
1128
|
-
}
|
|
1129
|
-
|
|
1130
|
-
|
|
1131
|
-
|
|
1132
|
-
|
|
1133
|
-
|
|
1134
|
-
|
|
1135
|
-
|
|
1136
|
-
|
|
1137
|
-
|
|
1138
|
-
|
|
1139
|
-
|
|
1140
|
-
|
|
1141
|
-
|
|
1142
|
-
|
|
1143
|
-
|
|
1133
|
+
},
|
|
1134
|
+
{
|
|
1135
|
+
column: "assembleCells.cloneContaminationPercents",
|
|
1136
|
+
id: "assemble-cells-clone-contamination-percents",
|
|
1137
|
+
allowNA: true,
|
|
1138
|
+
naRegex: "NaN",
|
|
1139
|
+
spec: {
|
|
1140
|
+
name: "mixcr.com/reports/assembleCells/cloneContaminationPercents",
|
|
1141
|
+
valueType: "Double",
|
|
1142
|
+
annotations: {
|
|
1143
|
+
"pl7.app/min": "0",
|
|
1144
|
+
"pl7.app/max": "100",
|
|
1145
|
+
"pl7.app/table/orderPriority": "64500",
|
|
1146
|
+
"pl7.app/table/visibility": "default",
|
|
1147
|
+
"pl7.app/label": "Clone Contamination (%)"
|
|
1148
|
+
}
|
|
1144
1149
|
}
|
|
1145
|
-
}
|
|
1146
|
-
|
|
1147
|
-
|
|
1148
|
-
|
|
1149
|
-
|
|
1150
|
-
|
|
1151
|
-
|
|
1152
|
-
|
|
1153
|
-
|
|
1154
|
-
|
|
1155
|
-
|
|
1156
|
-
|
|
1157
|
-
|
|
1158
|
-
|
|
1159
|
-
|
|
1150
|
+
},
|
|
1151
|
+
{
|
|
1152
|
+
column: "assembleCells.contaminatedCells",
|
|
1153
|
+
id: "assemble-cells-contaminated-cells",
|
|
1154
|
+
allowNA: true,
|
|
1155
|
+
naRegex: "NaN",
|
|
1156
|
+
spec: {
|
|
1157
|
+
name: "mixcr.com/reports/assembleCells/contaminatedCells",
|
|
1158
|
+
valueType: "Long",
|
|
1159
|
+
annotations: {
|
|
1160
|
+
"pl7.app/min": "0",
|
|
1161
|
+
"pl7.app/table/orderPriority": "64600",
|
|
1162
|
+
"pl7.app/table/visibility": "optional",
|
|
1163
|
+
"pl7.app/label": "Contaminated Cells"
|
|
1164
|
+
}
|
|
1160
1165
|
}
|
|
1161
|
-
}
|
|
1162
|
-
|
|
1163
|
-
|
|
1164
|
-
|
|
1165
|
-
|
|
1166
|
-
|
|
1167
|
-
|
|
1168
|
-
|
|
1169
|
-
|
|
1170
|
-
|
|
1171
|
-
|
|
1172
|
-
|
|
1173
|
-
|
|
1174
|
-
|
|
1175
|
-
|
|
1176
|
-
|
|
1166
|
+
},
|
|
1167
|
+
{
|
|
1168
|
+
column: "assembleCells.contaminatedCellsPercents",
|
|
1169
|
+
id: "assemble-cells-contaminated-cells-percents",
|
|
1170
|
+
allowNA: true,
|
|
1171
|
+
naRegex: "NaN",
|
|
1172
|
+
spec: {
|
|
1173
|
+
name: "mixcr.com/reports/assembleCells/contaminatedCellsPercents",
|
|
1174
|
+
valueType: "Double",
|
|
1175
|
+
annotations: {
|
|
1176
|
+
"pl7.app/min": "0",
|
|
1177
|
+
"pl7.app/max": "100",
|
|
1178
|
+
"pl7.app/table/orderPriority": "64700",
|
|
1179
|
+
"pl7.app/table/visibility": "default",
|
|
1180
|
+
"pl7.app/label": "Contaminated Cells (%)"
|
|
1181
|
+
}
|
|
1177
1182
|
}
|
|
1178
|
-
}
|
|
1179
|
-
|
|
1180
|
-
|
|
1181
|
-
|
|
1182
|
-
|
|
1183
|
-
|
|
1184
|
-
|
|
1185
|
-
|
|
1186
|
-
|
|
1187
|
-
|
|
1188
|
-
|
|
1189
|
-
|
|
1190
|
-
|
|
1191
|
-
|
|
1192
|
-
|
|
1183
|
+
},
|
|
1184
|
+
{
|
|
1185
|
+
column: "assembleCells.groupsWithTooMatchClones",
|
|
1186
|
+
id: "assemble-cells-groups-with-too-match-clones",
|
|
1187
|
+
allowNA: true,
|
|
1188
|
+
naRegex: "NaN",
|
|
1189
|
+
spec: {
|
|
1190
|
+
name: "mixcr.com/reports/assembleCells/groupsWithTooMatchClones",
|
|
1191
|
+
valueType: "Long",
|
|
1192
|
+
annotations: {
|
|
1193
|
+
"pl7.app/min": "0",
|
|
1194
|
+
"pl7.app/table/orderPriority": "64800",
|
|
1195
|
+
"pl7.app/table/visibility": "optional",
|
|
1196
|
+
"pl7.app/label": "Groups with Too Many Clones"
|
|
1197
|
+
}
|
|
1193
1198
|
}
|
|
1194
|
-
}
|
|
1195
|
-
|
|
1196
|
-
|
|
1197
|
-
|
|
1198
|
-
|
|
1199
|
-
|
|
1200
|
-
|
|
1201
|
-
|
|
1202
|
-
|
|
1203
|
-
|
|
1204
|
-
|
|
1205
|
-
|
|
1206
|
-
|
|
1207
|
-
|
|
1208
|
-
|
|
1209
|
-
|
|
1199
|
+
},
|
|
1200
|
+
{
|
|
1201
|
+
column: "assembleCells.groupsWithTooMatchClonesPercents",
|
|
1202
|
+
id: "assemble-cells-groups-with-too-match-clones-percents",
|
|
1203
|
+
allowNA: true,
|
|
1204
|
+
naRegex: "NaN",
|
|
1205
|
+
spec: {
|
|
1206
|
+
name: "mixcr.com/reports/assembleCells/groupsWithTooMatchClonesPercents",
|
|
1207
|
+
valueType: "Double",
|
|
1208
|
+
annotations: {
|
|
1209
|
+
"pl7.app/min": "0",
|
|
1210
|
+
"pl7.app/max": "100",
|
|
1211
|
+
"pl7.app/table/orderPriority": "64900",
|
|
1212
|
+
"pl7.app/table/visibility": "default",
|
|
1213
|
+
"pl7.app/label": "Groups with Too Many Clones (%)"
|
|
1214
|
+
}
|
|
1210
1215
|
}
|
|
1211
|
-
}
|
|
1212
|
-
|
|
1213
|
-
|
|
1214
|
-
|
|
1215
|
-
|
|
1216
|
-
|
|
1217
|
-
|
|
1218
|
-
|
|
1219
|
-
|
|
1220
|
-
|
|
1221
|
-
|
|
1222
|
-
|
|
1223
|
-
|
|
1224
|
-
|
|
1225
|
-
|
|
1216
|
+
},
|
|
1217
|
+
{
|
|
1218
|
+
column: "assembleCells.invalidGroups",
|
|
1219
|
+
id: "assemble-cells-invalid-groups",
|
|
1220
|
+
allowNA: true,
|
|
1221
|
+
naRegex: "NaN",
|
|
1222
|
+
spec: {
|
|
1223
|
+
name: "mixcr.com/reports/assembleCells/invalidGroups",
|
|
1224
|
+
valueType: "Long",
|
|
1225
|
+
annotations: {
|
|
1226
|
+
"pl7.app/min": "0",
|
|
1227
|
+
"pl7.app/table/orderPriority": "65000",
|
|
1228
|
+
"pl7.app/table/visibility": "optional",
|
|
1229
|
+
"pl7.app/label": "Invalid Groups"
|
|
1230
|
+
}
|
|
1226
1231
|
}
|
|
1227
|
-
}
|
|
1228
|
-
|
|
1229
|
-
|
|
1230
|
-
|
|
1231
|
-
|
|
1232
|
-
|
|
1233
|
-
|
|
1234
|
-
|
|
1235
|
-
|
|
1236
|
-
|
|
1237
|
-
|
|
1238
|
-
|
|
1239
|
-
|
|
1240
|
-
|
|
1241
|
-
|
|
1242
|
-
|
|
1232
|
+
},
|
|
1233
|
+
{
|
|
1234
|
+
column: "assembleCells.invalidGroupsPercents",
|
|
1235
|
+
id: "assemble-cells-invalid-groups-percents",
|
|
1236
|
+
allowNA: true,
|
|
1237
|
+
naRegex: "NaN",
|
|
1238
|
+
spec: {
|
|
1239
|
+
name: "mixcr.com/reports/assembleCells/invalidGroupsPercents",
|
|
1240
|
+
valueType: "Double",
|
|
1241
|
+
annotations: {
|
|
1242
|
+
"pl7.app/min": "0",
|
|
1243
|
+
"pl7.app/max": "100",
|
|
1244
|
+
"pl7.app/table/orderPriority": "65100",
|
|
1245
|
+
"pl7.app/table/visibility": "default",
|
|
1246
|
+
"pl7.app/label": "Invalid Groups (%)"
|
|
1247
|
+
}
|
|
1243
1248
|
}
|
|
1244
|
-
}
|
|
1245
|
-
|
|
1246
|
-
|
|
1247
|
-
|
|
1248
|
-
|
|
1249
|
-
|
|
1250
|
-
|
|
1251
|
-
|
|
1252
|
-
|
|
1253
|
-
|
|
1254
|
-
|
|
1255
|
-
|
|
1256
|
-
|
|
1257
|
-
|
|
1258
|
-
|
|
1249
|
+
},
|
|
1250
|
+
{
|
|
1251
|
+
column: "assembleCells.numberOfGroups",
|
|
1252
|
+
id: "assemble-cells-number-of-groups",
|
|
1253
|
+
allowNA: true,
|
|
1254
|
+
naRegex: "NaN",
|
|
1255
|
+
spec: {
|
|
1256
|
+
name: "mixcr.com/reports/assembleCells/numberOfGroups",
|
|
1257
|
+
valueType: "Long",
|
|
1258
|
+
annotations: {
|
|
1259
|
+
"pl7.app/min": "0",
|
|
1260
|
+
"pl7.app/table/orderPriority": "65200",
|
|
1261
|
+
"pl7.app/table/visibility": "optional",
|
|
1262
|
+
"pl7.app/label": "Number of Groups"
|
|
1263
|
+
}
|
|
1259
1264
|
}
|
|
1260
|
-
}
|
|
1261
|
-
|
|
1262
|
-
|
|
1263
|
-
|
|
1264
|
-
|
|
1265
|
-
|
|
1266
|
-
|
|
1267
|
-
|
|
1268
|
-
|
|
1269
|
-
|
|
1270
|
-
|
|
1271
|
-
|
|
1272
|
-
|
|
1273
|
-
|
|
1274
|
-
|
|
1265
|
+
},
|
|
1266
|
+
{
|
|
1267
|
+
column: "assembleCells.unassignedClonotypes",
|
|
1268
|
+
id: "assemble-cells-unassigned-clonotypes",
|
|
1269
|
+
allowNA: true,
|
|
1270
|
+
naRegex: "NaN",
|
|
1271
|
+
spec: {
|
|
1272
|
+
name: "mixcr.com/reports/assembleCells/unassignedClonotypes",
|
|
1273
|
+
valueType: "Long",
|
|
1274
|
+
annotations: {
|
|
1275
|
+
"pl7.app/min": "0",
|
|
1276
|
+
"pl7.app/table/orderPriority": "65300",
|
|
1277
|
+
"pl7.app/table/visibility": "optional",
|
|
1278
|
+
"pl7.app/label": "Unassigned Clonotypes"
|
|
1279
|
+
}
|
|
1275
1280
|
}
|
|
1276
|
-
}
|
|
1277
|
-
|
|
1278
|
-
|
|
1279
|
-
|
|
1280
|
-
|
|
1281
|
-
|
|
1282
|
-
|
|
1283
|
-
|
|
1284
|
-
|
|
1285
|
-
|
|
1286
|
-
|
|
1287
|
-
|
|
1288
|
-
|
|
1289
|
-
|
|
1290
|
-
|
|
1291
|
-
|
|
1281
|
+
},
|
|
1282
|
+
{
|
|
1283
|
+
column: "assembleCells.unassignedClonotypesPercents",
|
|
1284
|
+
id: "assemble-cells-unassigned-clonotypes-percents",
|
|
1285
|
+
allowNA: true,
|
|
1286
|
+
naRegex: "NaN",
|
|
1287
|
+
spec: {
|
|
1288
|
+
name: "mixcr.com/reports/assembleCells/unassignedClonotypesPercents",
|
|
1289
|
+
valueType: "Double",
|
|
1290
|
+
annotations: {
|
|
1291
|
+
"pl7.app/min": "0",
|
|
1292
|
+
"pl7.app/max": "100",
|
|
1293
|
+
"pl7.app/table/orderPriority": "65400",
|
|
1294
|
+
"pl7.app/table/visibility": "default",
|
|
1295
|
+
"pl7.app/label": "Unassigned Clonotypes (%)"
|
|
1296
|
+
}
|
|
1292
1297
|
}
|
|
1293
|
-
}
|
|
1294
|
-
}
|
|
1298
|
+
}]
|
|
1299
|
+
} // end if hasAssembleCells
|
|
1295
1300
|
|
|
1296
1301
|
|
|
1297
1302
|
scDropOrder := 107700
|