@platforma-open/milaboratories.mixcr-clonotyping-2.workflow 3.23.0 → 3.23.2
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/qc-report-columns.lib.tengo +238 -233
- 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 +4 -4
- package/src/calculate-preset-info.tpl.tengo +2 -0
- package/src/export-report.tpl.tengo +10 -1
- package/src/list-presets.tpl.tengo +1 -0
- package/src/mixcr-analyze.tpl.tengo +1 -0
- package/src/mixcr-export.tpl.tengo +1 -0
- package/src/qc-report-columns.lib.tengo +238 -233
package/.turbo/turbo-build.log
CHANGED
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@@ -1,6 +1,6 @@
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WARN Issue while reading "/home/runner/work/mixcr-clonotyping/mixcr-clonotyping/.npmrc". Failed to replace env in config: ${NPMJS_TOKEN}
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> @platforma-open/milaboratories.mixcr-clonotyping-2.workflow@3.23.
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> @platforma-open/milaboratories.mixcr-clonotyping-2.workflow@3.23.2 build /home/runner/work/mixcr-clonotyping/mixcr-clonotyping/workflow
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> shx rm -rf dist && pl-tengo check && pl-tengo build
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info: Skipping unknown file type: test/columns.test.ts
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package/CHANGELOG.md
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@@ -1,5 +1,17 @@
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# @platforma-open/milaboratories.mixcr-clonotyping.workflow
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## 3.23.2
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### Patch Changes
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- 40ec375: Upgrade MiXCR to 4.7.0-302-develop
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## 3.23.1
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### Patch Changes
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- 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
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## 3.23.0
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### Minor Changes
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@@ -6,7 +6,7 @@ pConstants := import("@platforma-sdk/workflow-tengo:pframes.constants")
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text := import("text")
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getQcReportColumns := func(hasUmi, isSingleCell, sampleIdAxisSpec, chains, cellTags, umiTags) {
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getQcReportColumns := func(hasUmi, isSingleCell, sampleIdAxisSpec, chains, cellTags, umiTags, hasAssembleCells) {
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if is_undefined(umiTags) {
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umiTags = []
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}
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@@ -1045,253 +1045,258 @@ getQcReportColumns := func(hasUmi, isSingleCell, sampleIdAxisSpec, chains, cellT
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]
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if hasAssembleCells {
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singleCellColumns += [
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{
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column: "assembleCells.cellBarcodesWithFoundGroups",
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id: "assemble-cells-cell-barcodes-with-found-groups",
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allowNA: true,
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naRegex: "NaN",
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spec: {
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name: "mixcr.com/reports/assembleCells/cellBarcodesWithFoundGroups",
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valueType: "Long",
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annotations: {
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"pl7.app/label": "Cell Barcodes with Found Groups"
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}
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},
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column: "assembleCells.cellBarcodesWithFoundGroupsPercents",
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id: "assemble-cells-cell-barcodes-with-found-groups-percents",
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naRegex: "NaN",
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spec: {
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name: "mixcr.com/reports/assembleCells/cellBarcodesWithFoundGroupsPercents",
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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": "Cell Barcodes with Found Groups (%)"
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}
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},
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column: "assembleCells.cellsNotIncludedBecauseContamination",
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id: "assemble-cells-cells-not-included-because-contamination",
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name: "mixcr.com/reports/assembleCells/cellsNotIncludedBecauseContamination",
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"pl7.app/label": "Cells Not Included Because Contamination"
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}
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id: "assemble-cells-groups-with-too-match-clones",
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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
|
|
Binary file
|
|
Binary file
|
|
Binary file
|
|
Binary file
|
|
Binary file
|
|
Binary file
|
|
Binary file
|
|
Binary file
|
|
Binary file
|
|
Binary file
|
|
Binary file
|
|
Binary file
|
package/package.json
CHANGED
|
@@ -1,13 +1,13 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@platforma-open/milaboratories.mixcr-clonotyping-2.workflow",
|
|
3
|
-
"version": "3.23.
|
|
3
|
+
"version": "3.23.2",
|
|
4
4
|
"description": "Tengo-based template",
|
|
5
5
|
"dependencies": {
|
|
6
|
-
"@platforma-sdk/workflow-tengo": "5.8.
|
|
7
|
-
"@platforma-open/milaboratories.software-mixcr": "4.7.0-
|
|
6
|
+
"@platforma-sdk/workflow-tengo": "5.8.2",
|
|
7
|
+
"@platforma-open/milaboratories.software-mixcr": "4.7.0-302-develop"
|
|
8
8
|
},
|
|
9
9
|
"devDependencies": {
|
|
10
|
-
"@platforma-sdk/tengo-builder": "2.4.
|
|
10
|
+
"@platforma-sdk/tengo-builder": "2.4.17"
|
|
11
11
|
},
|
|
12
12
|
"scripts": {
|
|
13
13
|
"build": "shx rm -rf dist && pl-tengo check && pl-tengo build",
|
|
@@ -39,6 +39,7 @@ self.body(func(inputs) {
|
|
|
39
39
|
software(mixcrSw).
|
|
40
40
|
env("MI_USE_SYSTEM_CA", "true").
|
|
41
41
|
secret("MI_LICENSE", "MI_LICENSE").
|
|
42
|
+
env("MI_LICENSE_DEBUG", "MI_LICENSE_DEBUG").
|
|
42
43
|
arg("exportPreset")
|
|
43
44
|
|
|
44
45
|
if smart.isResource(preset) /* file */ {
|
|
@@ -86,6 +87,7 @@ self.body(func(inputs) {
|
|
|
86
87
|
software(mixcrSw).
|
|
87
88
|
env("MI_USE_SYSTEM_CA", "true").
|
|
88
89
|
secret("MI_LICENSE", "MI_LICENSE").
|
|
90
|
+
env("MI_LICENSE_DEBUG", "MI_LICENSE_DEBUG").
|
|
89
91
|
arg("presetSpecificationsForBack").
|
|
90
92
|
addFile("preset.yaml", mixcrExportPresetCmd.getFile("preset.json")).
|
|
91
93
|
arg("preset.yaml").
|
|
@@ -36,6 +36,12 @@ self.body(func(inputs) {
|
|
|
36
36
|
umiTags := presetSpecForBack.umiTags
|
|
37
37
|
hasUmi := !is_undefined(umiTags) && len(umiTags) > 0
|
|
38
38
|
cellTags := presetSpecForBack.cellTags
|
|
39
|
+
hasAssembleCells := false
|
|
40
|
+
for stage in presetSpecForBack.analysisStages {
|
|
41
|
+
if stage == "assembleCells" {
|
|
42
|
+
hasAssembleCells = true
|
|
43
|
+
}
|
|
44
|
+
}
|
|
39
45
|
singleCellChainTsvsData := inputs.singleCellChainTsvsData
|
|
40
46
|
useStopCodonReplacement := !is_undefined(stopCodonTypes) && is_array(stopCodonTypes) && len(stopCodonTypes) > 0
|
|
41
47
|
if is_undefined(stopCodonReplacements) || !is_map(stopCodonReplacements) {
|
|
@@ -126,6 +132,7 @@ self.body(func(inputs) {
|
|
|
126
132
|
software(mixcrSw).
|
|
127
133
|
env("MI_USE_SYSTEM_CA", "true").
|
|
128
134
|
secret("MI_LICENSE", "MI_LICENSE").
|
|
135
|
+
env("MI_LICENSE_DEBUG", "MI_LICENSE_DEBUG").
|
|
129
136
|
arg("exportReportsTable")
|
|
130
137
|
|
|
131
138
|
// Add all clns files as input
|
|
@@ -206,6 +213,7 @@ self.body(func(inputs) {
|
|
|
206
213
|
software(mixcrSw).
|
|
207
214
|
env("MI_USE_SYSTEM_CA", "true").
|
|
208
215
|
secret("MI_LICENSE", "MI_LICENSE").
|
|
216
|
+
env("MI_LICENSE_DEBUG", "MI_LICENSE_DEBUG").
|
|
209
217
|
arg("exportClones").
|
|
210
218
|
arg("--dont-split-files").
|
|
211
219
|
arg("--drop-default-fields").
|
|
@@ -276,6 +284,7 @@ self.body(func(inputs) {
|
|
|
276
284
|
software(mixcrSw).
|
|
277
285
|
env("MI_USE_SYSTEM_CA", "true").
|
|
278
286
|
secret("MI_LICENSE", "MI_LICENSE").
|
|
287
|
+
env("MI_LICENSE_DEBUG", "MI_LICENSE_DEBUG").
|
|
279
288
|
arg("exportClones").
|
|
280
289
|
arg("--dont-split-files").
|
|
281
290
|
arg("--drop-default-fields").
|
|
@@ -493,7 +502,7 @@ self.body(func(inputs) {
|
|
|
493
502
|
|
|
494
503
|
tsvFile := wfResult.getFile("qc-report-processed.tsv")
|
|
495
504
|
|
|
496
|
-
qcReportColumns := qcReportColumns(hasUmi, isSingleCell, sampleIdAxisSpec, chains, cellTags, umiTags)
|
|
505
|
+
qcReportColumns := qcReportColumns(hasUmi, isSingleCell, sampleIdAxisSpec, chains, cellTags, umiTags, hasAssembleCells)
|
|
497
506
|
reportColumnsSpec := qcReportColumns.reportColumnsSpec
|
|
498
507
|
|
|
499
508
|
qcReportTable := xsv.importFile(
|
|
@@ -19,6 +19,7 @@ self.body(func(inputs) {
|
|
|
19
19
|
software(mixcrSw).
|
|
20
20
|
env("MI_USE_SYSTEM_CA", "true").
|
|
21
21
|
secret("MI_LICENSE", "MI_LICENSE").
|
|
22
|
+
env("MI_LICENSE_DEBUG", "MI_LICENSE_DEBUG").
|
|
22
23
|
arg("listPresetSpecificationsForUI").
|
|
23
24
|
arg("presets.json").
|
|
24
25
|
saveFile("presets.json").
|
|
@@ -6,7 +6,7 @@ pConstants := import("@platforma-sdk/workflow-tengo:pframes.constants")
|
|
|
6
6
|
text := import("text")
|
|
7
7
|
|
|
8
8
|
// QC Report column specifications function
|
|
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",
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|
|
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
|
// Single-cell per-chain dropped clonotypes by OOF / stop codons
|
|
1297
1302
|
scDropOrder := 107700
|