@platforma-open/milaboratories.mixcr-clonotyping-2.workflow 3.1.0 → 3.2.0
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 +216 -216
- 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 +2 -2
- package/src/calculate-export-specs.lib.tengo +2 -3
- package/src/process.tpl.tengo +9 -1
- package/src/qc-report-columns.lib.tengo +216 -216
package/.turbo/turbo-build.log
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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.
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> @platforma-open/milaboratories.mixcr-clonotyping-2.workflow@3.2.0 build /home/runner/work/mixcr-clonotyping/mixcr-clonotyping/workflow
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> 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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# @platforma-open/milaboratories.mixcr-clonotyping.workflow
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## 3.2.0
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### Minor Changes
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- 73af94c: nLengthTotalAdded column NA regex fix
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## 3.1.1
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### Patch Changes
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- 12d4102: Update sdk version
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## 3.1.0
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### Minor Changes
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@@ -545,12 +545,11 @@ calculateExportSpecs := func(presetSpecForBack, sampleIdAxisSpec, blockId) {
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junctionTypes := [ "VJ", "VD", "DJ" ]
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for junctionType in junctionTypes {
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feature := junctionType + "Junction"
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naRegex := junctionType == "VJ" ? "region_not_covered" : "no_d_gene"
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columnsSpecPerClonotypeNoAggregates += [ {
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column: "nLength" + feature,
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id: "n-length-" + text.to_lower(junctionType) + "-junction",
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naRegex:
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naRegex: "^[a-z_]*$",
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allowNA: true,
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spec: {
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name: "pl7.app/vdj/sequenceLength",
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columnsSpecPerClonotypeNoAggregates += [ {
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column: "nLengthTotalAdded",
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id: "n-length-total-added",
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naRegex: "
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naRegex: "^[a-z_]*$",
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allowNA: true,
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spec: {
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name: "pl7.app/vdj/sequenceLength",
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singleCellColumns := [
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@@ -1248,24 +1248,24 @@ getQcReportColumns := func(hasUmi, isSingleCell, sampleIdAxisSpec, chains) {
|
|
|
1248
1248
|
}
|
|
1249
1249
|
}]
|
|
1250
1250
|
|
|
1251
|
-
|
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1252
|
-
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1253
|
-
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1254
|
-
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1255
|
-
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1256
|
-
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1257
|
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1258
|
-
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|
1259
|
-
|
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1260
|
-
|
|
1261
|
-
|
|
1262
|
-
|
|
1263
|
-
|
|
1264
|
-
|
|
1265
|
-
|
|
1266
|
-
|
|
1267
|
-
|
|
1268
|
-
|
|
1251
|
+
|
|
1252
|
+
|
|
1253
|
+
|
|
1254
|
+
|
|
1255
|
+
|
|
1256
|
+
|
|
1257
|
+
|
|
1258
|
+
|
|
1259
|
+
|
|
1260
|
+
|
|
1261
|
+
|
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1262
|
+
|
|
1263
|
+
|
|
1264
|
+
|
|
1265
|
+
|
|
1266
|
+
|
|
1267
|
+
|
|
1268
|
+
|
|
1269
1269
|
|
|
1270
1270
|
columns := baseColumns
|
|
1271
1271
|
if hasUmi {
|
|
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.
|
|
3
|
+
"version": "3.2.0",
|
|
4
4
|
"description": "Tengo-based template",
|
|
5
5
|
"dependencies": {
|
|
6
6
|
"@platforma-sdk/workflow-tengo": "^5.0.3",
|
|
7
7
|
"@platforma-open/milaboratories.software-mixcr": "4.7.0-223-develop"
|
|
8
8
|
},
|
|
9
9
|
"devDependencies": {
|
|
10
|
-
"@platforma-sdk/tengo-builder": "^2.1.
|
|
10
|
+
"@platforma-sdk/tengo-builder": "^2.1.16",
|
|
11
11
|
"@platforma-sdk/test": "^1.42.20",
|
|
12
12
|
"vitest": "~2.1.9",
|
|
13
13
|
"typescript": "~5.6.3"
|
|
@@ -545,12 +545,11 @@ calculateExportSpecs := func(presetSpecForBack, sampleIdAxisSpec, blockId) {
|
|
|
545
545
|
junctionTypes := [ "VJ", "VD", "DJ" ]
|
|
546
546
|
for junctionType in junctionTypes {
|
|
547
547
|
feature := junctionType + "Junction"
|
|
548
|
-
naRegex := junctionType == "VJ" ? "region_not_covered" : "no_d_gene"
|
|
549
548
|
|
|
550
549
|
columnsSpecPerClonotypeNoAggregates += [ {
|
|
551
550
|
column: "nLength" + feature,
|
|
552
551
|
id: "n-length-" + text.to_lower(junctionType) + "-junction",
|
|
553
|
-
naRegex:
|
|
552
|
+
naRegex: "^[a-z_]*$",
|
|
554
553
|
allowNA: true,
|
|
555
554
|
spec: {
|
|
556
555
|
name: "pl7.app/vdj/sequenceLength",
|
|
@@ -572,7 +571,7 @@ calculateExportSpecs := func(presetSpecForBack, sampleIdAxisSpec, blockId) {
|
|
|
572
571
|
columnsSpecPerClonotypeNoAggregates += [ {
|
|
573
572
|
column: "nLengthTotalAdded",
|
|
574
573
|
id: "n-length-total-added",
|
|
575
|
-
naRegex: "
|
|
574
|
+
naRegex: "^[a-z_]*$",
|
|
576
575
|
allowNA: true,
|
|
577
576
|
spec: {
|
|
578
577
|
name: "pl7.app/vdj/sequenceLength",
|
package/src/process.tpl.tengo
CHANGED
|
@@ -675,7 +675,15 @@ self.body(func(inputs) {
|
|
|
675
675
|
singleCellResult.addXsvOutputToBuilder(clonotypes, "propertiesBPrimary", "clonotypeProperties/" + receptor + "/bPrimary/")
|
|
676
676
|
singleCellResult.addXsvOutputToBuilder(clonotypes, "propertiesBSecondary", "clonotypeProperties/" + receptor + "/bSecondary/")
|
|
677
677
|
|
|
678
|
-
singleCellResult.
|
|
678
|
+
for columnName in singleCellResult.listXsvColumns("cellsLinkerTable") {
|
|
679
|
+
anonymizedData := singleCellResult.outputData("cellsLinkerTable", columnName)
|
|
680
|
+
clonotypes.add(
|
|
681
|
+
"clonotypeProperties/" + receptor + "/cellsLinkerTable/" + columnName,
|
|
682
|
+
singleCellResult.outputSpec("cellsLinkerTable", columnName),
|
|
683
|
+
anonymize.deanonymizePKeys(anonymizedData, 0, [0], anonymizationResult.mapping)
|
|
684
|
+
)
|
|
685
|
+
resultsToCache["clonotypeProperties/" + receptor + "/cellsLinkerTable/" + columnName] = anonymizedData
|
|
686
|
+
}
|
|
679
687
|
}
|
|
680
688
|
}
|
|
681
689
|
|
|
@@ -736,204 +736,204 @@ getQcReportColumns := func(hasUmi, isSingleCell, sampleIdAxisSpec, chains) {
|
|
|
736
736
|
|
|
737
737
|
// Single Cell columns
|
|
738
738
|
singleCellColumns := [
|
|
739
|
-
{
|
|
740
|
-
|
|
741
|
-
|
|
742
|
-
|
|
743
|
-
|
|
744
|
-
|
|
745
|
-
|
|
746
|
-
|
|
747
|
-
|
|
748
|
-
|
|
749
|
-
|
|
750
|
-
|
|
751
|
-
|
|
752
|
-
|
|
753
|
-
|
|
754
|
-
},
|
|
755
|
-
{
|
|
756
|
-
|
|
757
|
-
|
|
758
|
-
|
|
759
|
-
|
|
760
|
-
|
|
761
|
-
|
|
762
|
-
|
|
763
|
-
|
|
764
|
-
|
|
765
|
-
|
|
766
|
-
|
|
767
|
-
|
|
768
|
-
|
|
769
|
-
|
|
770
|
-
|
|
771
|
-
},
|
|
772
|
-
{
|
|
773
|
-
|
|
774
|
-
|
|
775
|
-
|
|
776
|
-
|
|
777
|
-
|
|
778
|
-
|
|
779
|
-
|
|
780
|
-
|
|
781
|
-
|
|
782
|
-
|
|
783
|
-
|
|
784
|
-
|
|
785
|
-
|
|
786
|
-
|
|
787
|
-
},
|
|
788
|
-
{
|
|
789
|
-
|
|
790
|
-
|
|
791
|
-
|
|
792
|
-
|
|
793
|
-
|
|
794
|
-
|
|
795
|
-
|
|
796
|
-
|
|
797
|
-
|
|
798
|
-
|
|
799
|
-
|
|
800
|
-
|
|
801
|
-
|
|
802
|
-
|
|
803
|
-
|
|
804
|
-
},
|
|
805
|
-
{
|
|
806
|
-
|
|
807
|
-
|
|
808
|
-
|
|
809
|
-
|
|
810
|
-
|
|
811
|
-
|
|
812
|
-
|
|
813
|
-
|
|
814
|
-
|
|
815
|
-
|
|
816
|
-
|
|
817
|
-
|
|
818
|
-
|
|
819
|
-
|
|
820
|
-
},
|
|
821
|
-
{
|
|
822
|
-
|
|
823
|
-
|
|
824
|
-
|
|
825
|
-
|
|
826
|
-
|
|
827
|
-
|
|
828
|
-
|
|
829
|
-
|
|
830
|
-
|
|
831
|
-
|
|
832
|
-
|
|
833
|
-
|
|
834
|
-
|
|
835
|
-
|
|
836
|
-
|
|
837
|
-
},
|
|
838
|
-
{
|
|
839
|
-
|
|
840
|
-
|
|
841
|
-
|
|
842
|
-
|
|
843
|
-
|
|
844
|
-
|
|
845
|
-
|
|
846
|
-
|
|
847
|
-
|
|
848
|
-
|
|
849
|
-
|
|
850
|
-
|
|
851
|
-
|
|
852
|
-
|
|
853
|
-
},
|
|
854
|
-
{
|
|
855
|
-
|
|
856
|
-
|
|
857
|
-
|
|
858
|
-
|
|
859
|
-
|
|
860
|
-
|
|
861
|
-
|
|
862
|
-
|
|
863
|
-
|
|
864
|
-
|
|
865
|
-
|
|
866
|
-
|
|
867
|
-
|
|
868
|
-
|
|
869
|
-
|
|
870
|
-
},
|
|
871
|
-
{
|
|
872
|
-
|
|
873
|
-
|
|
874
|
-
|
|
875
|
-
|
|
876
|
-
|
|
877
|
-
|
|
878
|
-
|
|
879
|
-
|
|
880
|
-
|
|
881
|
-
|
|
882
|
-
|
|
883
|
-
|
|
884
|
-
|
|
885
|
-
|
|
886
|
-
},
|
|
887
|
-
{
|
|
888
|
-
|
|
889
|
-
|
|
890
|
-
|
|
891
|
-
|
|
892
|
-
|
|
893
|
-
|
|
894
|
-
|
|
895
|
-
|
|
896
|
-
|
|
897
|
-
|
|
898
|
-
|
|
899
|
-
|
|
900
|
-
|
|
901
|
-
|
|
902
|
-
|
|
903
|
-
},
|
|
904
|
-
{
|
|
905
|
-
|
|
906
|
-
|
|
907
|
-
|
|
908
|
-
|
|
909
|
-
|
|
910
|
-
|
|
911
|
-
|
|
912
|
-
|
|
913
|
-
|
|
914
|
-
|
|
915
|
-
|
|
916
|
-
|
|
917
|
-
|
|
918
|
-
|
|
919
|
-
},
|
|
920
|
-
{
|
|
921
|
-
|
|
922
|
-
|
|
923
|
-
|
|
924
|
-
|
|
925
|
-
|
|
926
|
-
|
|
927
|
-
|
|
928
|
-
|
|
929
|
-
|
|
930
|
-
|
|
931
|
-
|
|
932
|
-
|
|
933
|
-
|
|
934
|
-
|
|
935
|
-
|
|
936
|
-
},
|
|
739
|
+
// {
|
|
740
|
+
// column: "align.readsWithChain.IGH",
|
|
741
|
+
// id: "align-reads-with-chain-igh",
|
|
742
|
+
// allowNA: true,
|
|
743
|
+
// naRegex: "",
|
|
744
|
+
// spec: {
|
|
745
|
+
// name: "mixcr.com/reports/align/readsWithChain/IGH",
|
|
746
|
+
// valueType: "Long",
|
|
747
|
+
// annotations: {
|
|
748
|
+
// "pl7.app/min": "0",
|
|
749
|
+
// "pl7.app/table/orderPriority": "96000",
|
|
750
|
+
// "pl7.app/table/visibility": "optional",
|
|
751
|
+
// "pl7.app/label": "Reads with Chain IGH"
|
|
752
|
+
// }
|
|
753
|
+
// }
|
|
754
|
+
// },
|
|
755
|
+
// {
|
|
756
|
+
// column: "align.readsWithChain.IGHPercents",
|
|
757
|
+
// id: "align-reads-with-chain-igh-percents",
|
|
758
|
+
// allowNA: true,
|
|
759
|
+
// naRegex: "",
|
|
760
|
+
// spec: {
|
|
761
|
+
// name: "mixcr.com/reports/align/readsWithChain/IGHPercents",
|
|
762
|
+
// valueType: "Double",
|
|
763
|
+
// annotations: {
|
|
764
|
+
// "pl7.app/min": "0",
|
|
765
|
+
// "pl7.app/max": "100",
|
|
766
|
+
// "pl7.app/table/orderPriority": "96100",
|
|
767
|
+
// "pl7.app/table/visibility": "default",
|
|
768
|
+
// "pl7.app/label": "Reads with Chain IGH (%)"
|
|
769
|
+
// }
|
|
770
|
+
// }
|
|
771
|
+
// },
|
|
772
|
+
// {
|
|
773
|
+
// column: "align.readsWithChain.IGK",
|
|
774
|
+
// id: "align-reads-with-chain-igk",
|
|
775
|
+
// allowNA: true,
|
|
776
|
+
// naRegex: "",
|
|
777
|
+
// spec: {
|
|
778
|
+
// name: "mixcr.com/reports/align/readsWithChain/IGK",
|
|
779
|
+
// valueType: "Long",
|
|
780
|
+
// annotations: {
|
|
781
|
+
// "pl7.app/min": "0",
|
|
782
|
+
// "pl7.app/table/orderPriority": "96200",
|
|
783
|
+
// "pl7.app/table/visibility": "optional",
|
|
784
|
+
// "pl7.app/label": "Reads with Chain IGK"
|
|
785
|
+
// }
|
|
786
|
+
// }
|
|
787
|
+
// },
|
|
788
|
+
// {
|
|
789
|
+
// column: "align.readsWithChain.IGKPercents",
|
|
790
|
+
// id: "align-reads-with-chain-igk-percents",
|
|
791
|
+
// allowNA: true,
|
|
792
|
+
// naRegex: "",
|
|
793
|
+
// spec: {
|
|
794
|
+
// name: "mixcr.com/reports/align/readsWithChain/IGKPercents",
|
|
795
|
+
// valueType: "Double",
|
|
796
|
+
// annotations: {
|
|
797
|
+
// "pl7.app/min": "0",
|
|
798
|
+
// "pl7.app/max": "100",
|
|
799
|
+
// "pl7.app/table/orderPriority": "96300",
|
|
800
|
+
// "pl7.app/table/visibility": "default",
|
|
801
|
+
// "pl7.app/label": "Reads with Chain IGK (%)"
|
|
802
|
+
// }
|
|
803
|
+
// }
|
|
804
|
+
// },
|
|
805
|
+
// {
|
|
806
|
+
// column: "align.readsWithChain.IGL",
|
|
807
|
+
// id: "align-reads-with-chain-igl",
|
|
808
|
+
// allowNA: true,
|
|
809
|
+
// naRegex: "",
|
|
810
|
+
// spec: {
|
|
811
|
+
// name: "mixcr.com/reports/align/readsWithChain/IGL",
|
|
812
|
+
// valueType: "Long",
|
|
813
|
+
// annotations: {
|
|
814
|
+
// "pl7.app/min": "0",
|
|
815
|
+
// "pl7.app/table/orderPriority": "96400",
|
|
816
|
+
// "pl7.app/table/visibility": "optional",
|
|
817
|
+
// "pl7.app/label": "Reads with Chain IGL"
|
|
818
|
+
// }
|
|
819
|
+
// }
|
|
820
|
+
// },
|
|
821
|
+
// {
|
|
822
|
+
// column: "align.readsWithChain.IGLPercents",
|
|
823
|
+
// id: "align-reads-with-chain-igl-percents",
|
|
824
|
+
// allowNA: true,
|
|
825
|
+
// naRegex: "",
|
|
826
|
+
// spec: {
|
|
827
|
+
// name: "mixcr.com/reports/align/readsWithChain/IGLPercents",
|
|
828
|
+
// valueType: "Double",
|
|
829
|
+
// annotations: {
|
|
830
|
+
// "pl7.app/min": "0",
|
|
831
|
+
// "pl7.app/max": "100",
|
|
832
|
+
// "pl7.app/table/orderPriority": "96500",
|
|
833
|
+
// "pl7.app/table/visibility": "default",
|
|
834
|
+
// "pl7.app/label": "Reads with Chain IGL (%)"
|
|
835
|
+
// }
|
|
836
|
+
// }
|
|
837
|
+
// },
|
|
838
|
+
// {
|
|
839
|
+
// column: "align.readsWithChain.TRAD",
|
|
840
|
+
// id: "align-reads-with-chain-trad",
|
|
841
|
+
// allowNA: true,
|
|
842
|
+
// naRegex: "",
|
|
843
|
+
// spec: {
|
|
844
|
+
// name: "mixcr.com/reports/align/readsWithChain/TRAD",
|
|
845
|
+
// valueType: "Long",
|
|
846
|
+
// annotations: {
|
|
847
|
+
// "pl7.app/min": "0",
|
|
848
|
+
// "pl7.app/table/orderPriority": "96700",
|
|
849
|
+
// "pl7.app/table/visibility": "optional",
|
|
850
|
+
// "pl7.app/label": "Reads with Chain TRAD"
|
|
851
|
+
// }
|
|
852
|
+
// }
|
|
853
|
+
// },
|
|
854
|
+
// {
|
|
855
|
+
// column: "align.readsWithChain.TRADPercents",
|
|
856
|
+
// id: "align-reads-with-chain-trad-percents",
|
|
857
|
+
// allowNA: true,
|
|
858
|
+
// naRegex: "",
|
|
859
|
+
// spec: {
|
|
860
|
+
// name: "mixcr.com/reports/align/readsWithChain/TRADPercents",
|
|
861
|
+
// valueType: "Double",
|
|
862
|
+
// annotations: {
|
|
863
|
+
// "pl7.app/min": "0",
|
|
864
|
+
// "pl7.app/max": "100",
|
|
865
|
+
// "pl7.app/table/orderPriority": "96800",
|
|
866
|
+
// "pl7.app/table/visibility": "default",
|
|
867
|
+
// "pl7.app/label": "Reads with Chain TRAD (%)"
|
|
868
|
+
// }
|
|
869
|
+
// }
|
|
870
|
+
// },
|
|
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",
|
|
@@ -1248,24 +1248,24 @@ getQcReportColumns := func(hasUmi, isSingleCell, sampleIdAxisSpec, chains) {
|
|
|
1248
1248
|
}
|
|
1249
1249
|
}]
|
|
1250
1250
|
|
|
1251
|
-
for chain in chains {
|
|
1252
|
-
|
|
1253
|
-
|
|
1254
|
-
|
|
1255
|
-
|
|
1256
|
-
|
|
1257
|
-
|
|
1258
|
-
|
|
1259
|
-
|
|
1260
|
-
|
|
1261
|
-
|
|
1262
|
-
|
|
1263
|
-
|
|
1264
|
-
|
|
1265
|
-
|
|
1266
|
-
|
|
1267
|
-
|
|
1268
|
-
}
|
|
1251
|
+
// for chain in chains {
|
|
1252
|
+
// singleCellColumns += [{
|
|
1253
|
+
// column: "clonesWithChain." + chain,
|
|
1254
|
+
// id: "clones-with-chain-" + chain,
|
|
1255
|
+
// allowNA: true,
|
|
1256
|
+
// naRegex: "",
|
|
1257
|
+
// spec: {
|
|
1258
|
+
// name: "mixcr.com/reports/clonesWithChain/" + chain,
|
|
1259
|
+
// valueType: "Long",
|
|
1260
|
+
// annotations: {
|
|
1261
|
+
// "pl7.app/min": "0",
|
|
1262
|
+
// "pl7.app/table/orderPriority": "97400",
|
|
1263
|
+
// "pl7.app/table/visibility": "optional",
|
|
1264
|
+
// "pl7.app/label": "Clones with Chain " + chain
|
|
1265
|
+
// }
|
|
1266
|
+
// }
|
|
1267
|
+
// }]
|
|
1268
|
+
// }
|
|
1269
1269
|
|
|
1270
1270
|
columns := baseColumns
|
|
1271
1271
|
if hasUmi {
|