@platforma-open/milaboratories.mixcr-clonotyping-2.workflow 3.21.0 → 3.22.0
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 +6 -0
- package/dist/tengo/lib/qc-report-columns.lib.tengo +77 -64
- 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/export-report.tpl.tengo +3 -2
- package/src/qc-report-columns.lib.tengo +77 -64
package/.turbo/turbo-build.log
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
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.
|
|
3
|
+
> @platforma-open/milaboratories.mixcr-clonotyping-2.workflow@3.22.0 build /home/runner/work/mixcr-clonotyping/mixcr-clonotyping/workflow
|
|
4
4
|
> rm -rf dist && pl-tengo check && pl-tengo build
|
|
5
5
|
|
|
6
6
|
info: Skipping unknown file type: test/columns.test.ts
|
package/CHANGELOG.md
CHANGED
|
@@ -3,9 +3,13 @@
|
|
|
3
3
|
|
|
4
4
|
ll := import("@platforma-sdk/workflow-tengo:ll")
|
|
5
5
|
pConstants := import("@platforma-sdk/workflow-tengo:pframes.constants")
|
|
6
|
+
text := import("text")
|
|
6
7
|
|
|
7
8
|
|
|
8
|
-
getQcReportColumns := func(hasUmi, isSingleCell, sampleIdAxisSpec, chains, cellTags) {
|
|
9
|
+
getQcReportColumns := func(hasUmi, isSingleCell, sampleIdAxisSpec, chains, cellTags, umiTags) {
|
|
10
|
+
if is_undefined(umiTags) {
|
|
11
|
+
umiTags = []
|
|
12
|
+
}
|
|
9
13
|
|
|
10
14
|
baseColumns := [
|
|
11
15
|
{
|
|
@@ -656,73 +660,82 @@ getQcReportColumns := func(hasUmi, isSingleCell, sampleIdAxisSpec, chains, cellT
|
|
|
656
660
|
}
|
|
657
661
|
}
|
|
658
662
|
|
|
659
|
-
dataWithUmiColumns := [
|
|
660
|
-
|
|
661
|
-
|
|
662
|
-
|
|
663
|
-
|
|
664
|
-
|
|
665
|
-
|
|
666
|
-
|
|
667
|
-
|
|
668
|
-
|
|
669
|
-
|
|
670
|
-
|
|
671
|
-
|
|
663
|
+
dataWithUmiColumns := []
|
|
664
|
+
for idx, umiTag in umiTags {
|
|
665
|
+
orderBase := 85000 + idx * 10
|
|
666
|
+
orderBasePercents := 85100 + idx * 10
|
|
667
|
+
orderDiversity := 85200 + idx * 10
|
|
668
|
+
orderDiversityPercents := 85300 + idx * 10
|
|
669
|
+
tagL := text.to_lower(umiTag)
|
|
670
|
+
dataWithUmiColumns = dataWithUmiColumns + [{
|
|
671
|
+
column: "refineTags." + umiTag + ".outputCount",
|
|
672
|
+
id: "refine-tags-" + tagL + "-output-count",
|
|
673
|
+
allowNA: true,
|
|
674
|
+
naRegex: "NaN",
|
|
675
|
+
spec: {
|
|
676
|
+
name: "mixcr.com/reports/refineTags/" + umiTag + "/outputCount",
|
|
677
|
+
valueType: "Long",
|
|
678
|
+
annotations: {
|
|
679
|
+
"pl7.app/min": "0",
|
|
680
|
+
"pl7.app/table/orderPriority": string(orderBase),
|
|
681
|
+
"pl7.app/table/visibility": "optional",
|
|
682
|
+
"pl7.app/label": "Refine Tags " + umiTag + " - Output Count"
|
|
683
|
+
}
|
|
672
684
|
}
|
|
673
|
-
}
|
|
674
|
-
|
|
675
|
-
|
|
676
|
-
|
|
677
|
-
|
|
678
|
-
|
|
679
|
-
|
|
680
|
-
|
|
681
|
-
|
|
682
|
-
|
|
683
|
-
|
|
684
|
-
|
|
685
|
-
|
|
686
|
-
|
|
687
|
-
|
|
688
|
-
|
|
685
|
+
},
|
|
686
|
+
{
|
|
687
|
+
column: "refineTags." + umiTag + ".outputCountPercents",
|
|
688
|
+
id: "refine-tags-" + tagL + "-output-count-percents",
|
|
689
|
+
allowNA: true,
|
|
690
|
+
naRegex: "NaN",
|
|
691
|
+
spec: {
|
|
692
|
+
name: "mixcr.com/reports/refineTags/" + umiTag + "/outputCountPercents",
|
|
693
|
+
valueType: "Double",
|
|
694
|
+
annotations: {
|
|
695
|
+
"pl7.app/min": "0",
|
|
696
|
+
"pl7.app/max": "100",
|
|
697
|
+
"pl7.app/table/orderPriority": string(orderBasePercents),
|
|
698
|
+
"pl7.app/table/visibility": "default",
|
|
699
|
+
"pl7.app/label": "Refine Tags " + umiTag + " - Output Count (%)"
|
|
700
|
+
}
|
|
689
701
|
}
|
|
690
|
-
}
|
|
691
|
-
|
|
692
|
-
|
|
693
|
-
|
|
694
|
-
|
|
695
|
-
|
|
696
|
-
|
|
697
|
-
|
|
698
|
-
|
|
699
|
-
|
|
700
|
-
|
|
701
|
-
|
|
702
|
-
|
|
703
|
-
|
|
704
|
-
|
|
702
|
+
},
|
|
703
|
+
{
|
|
704
|
+
column: "refineTags." + umiTag + ".outputDiversity",
|
|
705
|
+
id: "refine-tags-" + tagL + "-output-diversity",
|
|
706
|
+
allowNA: true,
|
|
707
|
+
naRegex: "NaN",
|
|
708
|
+
spec: {
|
|
709
|
+
name: "mixcr.com/reports/refineTags/" + umiTag + "/outputDiversity",
|
|
710
|
+
valueType: "Long",
|
|
711
|
+
annotations: {
|
|
712
|
+
"pl7.app/min": "0",
|
|
713
|
+
"pl7.app/table/orderPriority": string(orderDiversity),
|
|
714
|
+
"pl7.app/table/visibility": "optional",
|
|
715
|
+
"pl7.app/label": "Refine Tags " + umiTag + " - Output Diversity"
|
|
716
|
+
}
|
|
705
717
|
}
|
|
706
|
-
}
|
|
707
|
-
|
|
708
|
-
|
|
709
|
-
|
|
710
|
-
|
|
711
|
-
|
|
712
|
-
|
|
713
|
-
|
|
714
|
-
|
|
715
|
-
|
|
716
|
-
|
|
717
|
-
|
|
718
|
-
|
|
719
|
-
|
|
720
|
-
|
|
721
|
-
|
|
718
|
+
},
|
|
719
|
+
{
|
|
720
|
+
column: "refineTags." + umiTag + ".outputDiversityPercents",
|
|
721
|
+
id: "refine-tags-" + tagL + "-output-diversity-percents",
|
|
722
|
+
allowNA: true,
|
|
723
|
+
naRegex: "NaN",
|
|
724
|
+
spec: {
|
|
725
|
+
name: "mixcr.com/reports/refineTags/" + umiTag + "/outputDiversityPercents",
|
|
726
|
+
valueType: "Double",
|
|
727
|
+
annotations: {
|
|
728
|
+
"pl7.app/min": "0",
|
|
729
|
+
"pl7.app/max": "100",
|
|
730
|
+
"pl7.app/table/orderPriority": string(orderDiversityPercents),
|
|
731
|
+
"pl7.app/table/visibility": "default",
|
|
732
|
+
"pl7.app/label": "Refine Tags " + umiTag + " - Output Diversity (%)"
|
|
733
|
+
}
|
|
722
734
|
}
|
|
723
|
-
}
|
|
724
|
-
}
|
|
725
|
-
|
|
735
|
+
}]
|
|
736
|
+
}
|
|
737
|
+
|
|
738
|
+
dataWithUmiColumns = dataWithUmiColumns + [{
|
|
726
739
|
column: "refineTags.numberOfGroupsAccepted",
|
|
727
740
|
id: "refine-tags-number-of-groups-accepted",
|
|
728
741
|
allowNA: true,
|
|
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
|
@@ -31,7 +31,8 @@ self.body(func(inputs) {
|
|
|
31
31
|
clonotypeTablesData := inputs.clonotypeTablesData
|
|
32
32
|
|
|
33
33
|
isSingleCell := len(presetSpecForBack.cellTags) > 0
|
|
34
|
-
|
|
34
|
+
umiTags := presetSpecForBack.umiTags
|
|
35
|
+
hasUmi := !is_undefined(umiTags) && len(umiTags) > 0
|
|
35
36
|
cellTags := presetSpecForBack.cellTags
|
|
36
37
|
singleCellChainTsvsData := inputs.singleCellChainTsvsData
|
|
37
38
|
|
|
@@ -409,7 +410,7 @@ self.body(func(inputs) {
|
|
|
409
410
|
|
|
410
411
|
tsvFile := wfResult.getFile("qc-report-processed.tsv")
|
|
411
412
|
|
|
412
|
-
qcReportColumns := qcReportColumns(hasUmi, isSingleCell, sampleIdAxisSpec, chains, cellTags)
|
|
413
|
+
qcReportColumns := qcReportColumns(hasUmi, isSingleCell, sampleIdAxisSpec, chains, cellTags, umiTags)
|
|
413
414
|
reportColumnsSpec := qcReportColumns.reportColumnsSpec
|
|
414
415
|
|
|
415
416
|
qcReportTable := xsv.importFile(
|
|
@@ -3,9 +3,13 @@
|
|
|
3
3
|
|
|
4
4
|
ll := import("@platforma-sdk/workflow-tengo:ll")
|
|
5
5
|
pConstants := import("@platforma-sdk/workflow-tengo:pframes.constants")
|
|
6
|
+
text := import("text")
|
|
6
7
|
|
|
7
8
|
// QC Report column specifications function
|
|
8
|
-
getQcReportColumns := func(hasUmi, isSingleCell, sampleIdAxisSpec, chains, cellTags) {
|
|
9
|
+
getQcReportColumns := func(hasUmi, isSingleCell, sampleIdAxisSpec, chains, cellTags, umiTags) {
|
|
10
|
+
if is_undefined(umiTags) {
|
|
11
|
+
umiTags = []
|
|
12
|
+
}
|
|
9
13
|
// Bulk sequencing columns
|
|
10
14
|
baseColumns := [
|
|
11
15
|
{
|
|
@@ -656,73 +660,82 @@ getQcReportColumns := func(hasUmi, isSingleCell, sampleIdAxisSpec, chains, cellT
|
|
|
656
660
|
}
|
|
657
661
|
}
|
|
658
662
|
|
|
659
|
-
dataWithUmiColumns := [
|
|
660
|
-
|
|
661
|
-
|
|
662
|
-
|
|
663
|
-
|
|
664
|
-
|
|
665
|
-
|
|
666
|
-
|
|
667
|
-
|
|
668
|
-
|
|
669
|
-
|
|
670
|
-
|
|
671
|
-
|
|
663
|
+
dataWithUmiColumns := []
|
|
664
|
+
for idx, umiTag in umiTags {
|
|
665
|
+
orderBase := 85000 + idx * 10
|
|
666
|
+
orderBasePercents := 85100 + idx * 10
|
|
667
|
+
orderDiversity := 85200 + idx * 10
|
|
668
|
+
orderDiversityPercents := 85300 + idx * 10
|
|
669
|
+
tagL := text.to_lower(umiTag)
|
|
670
|
+
dataWithUmiColumns = dataWithUmiColumns + [{
|
|
671
|
+
column: "refineTags." + umiTag + ".outputCount",
|
|
672
|
+
id: "refine-tags-" + tagL + "-output-count",
|
|
673
|
+
allowNA: true,
|
|
674
|
+
naRegex: "NaN",
|
|
675
|
+
spec: {
|
|
676
|
+
name: "mixcr.com/reports/refineTags/" + umiTag + "/outputCount",
|
|
677
|
+
valueType: "Long",
|
|
678
|
+
annotations: {
|
|
679
|
+
"pl7.app/min": "0",
|
|
680
|
+
"pl7.app/table/orderPriority": string(orderBase),
|
|
681
|
+
"pl7.app/table/visibility": "optional",
|
|
682
|
+
"pl7.app/label": "Refine Tags " + umiTag + " - Output Count"
|
|
683
|
+
}
|
|
672
684
|
}
|
|
673
|
-
}
|
|
674
|
-
|
|
675
|
-
|
|
676
|
-
|
|
677
|
-
|
|
678
|
-
|
|
679
|
-
|
|
680
|
-
|
|
681
|
-
|
|
682
|
-
|
|
683
|
-
|
|
684
|
-
|
|
685
|
-
|
|
686
|
-
|
|
687
|
-
|
|
688
|
-
|
|
685
|
+
},
|
|
686
|
+
{
|
|
687
|
+
column: "refineTags." + umiTag + ".outputCountPercents",
|
|
688
|
+
id: "refine-tags-" + tagL + "-output-count-percents",
|
|
689
|
+
allowNA: true,
|
|
690
|
+
naRegex: "NaN",
|
|
691
|
+
spec: {
|
|
692
|
+
name: "mixcr.com/reports/refineTags/" + umiTag + "/outputCountPercents",
|
|
693
|
+
valueType: "Double",
|
|
694
|
+
annotations: {
|
|
695
|
+
"pl7.app/min": "0",
|
|
696
|
+
"pl7.app/max": "100",
|
|
697
|
+
"pl7.app/table/orderPriority": string(orderBasePercents),
|
|
698
|
+
"pl7.app/table/visibility": "default",
|
|
699
|
+
"pl7.app/label": "Refine Tags " + umiTag + " - Output Count (%)"
|
|
700
|
+
}
|
|
689
701
|
}
|
|
690
|
-
}
|
|
691
|
-
|
|
692
|
-
|
|
693
|
-
|
|
694
|
-
|
|
695
|
-
|
|
696
|
-
|
|
697
|
-
|
|
698
|
-
|
|
699
|
-
|
|
700
|
-
|
|
701
|
-
|
|
702
|
-
|
|
703
|
-
|
|
704
|
-
|
|
702
|
+
},
|
|
703
|
+
{
|
|
704
|
+
column: "refineTags." + umiTag + ".outputDiversity",
|
|
705
|
+
id: "refine-tags-" + tagL + "-output-diversity",
|
|
706
|
+
allowNA: true,
|
|
707
|
+
naRegex: "NaN",
|
|
708
|
+
spec: {
|
|
709
|
+
name: "mixcr.com/reports/refineTags/" + umiTag + "/outputDiversity",
|
|
710
|
+
valueType: "Long",
|
|
711
|
+
annotations: {
|
|
712
|
+
"pl7.app/min": "0",
|
|
713
|
+
"pl7.app/table/orderPriority": string(orderDiversity),
|
|
714
|
+
"pl7.app/table/visibility": "optional",
|
|
715
|
+
"pl7.app/label": "Refine Tags " + umiTag + " - Output Diversity"
|
|
716
|
+
}
|
|
705
717
|
}
|
|
706
|
-
}
|
|
707
|
-
|
|
708
|
-
|
|
709
|
-
|
|
710
|
-
|
|
711
|
-
|
|
712
|
-
|
|
713
|
-
|
|
714
|
-
|
|
715
|
-
|
|
716
|
-
|
|
717
|
-
|
|
718
|
-
|
|
719
|
-
|
|
720
|
-
|
|
721
|
-
|
|
718
|
+
},
|
|
719
|
+
{
|
|
720
|
+
column: "refineTags." + umiTag + ".outputDiversityPercents",
|
|
721
|
+
id: "refine-tags-" + tagL + "-output-diversity-percents",
|
|
722
|
+
allowNA: true,
|
|
723
|
+
naRegex: "NaN",
|
|
724
|
+
spec: {
|
|
725
|
+
name: "mixcr.com/reports/refineTags/" + umiTag + "/outputDiversityPercents",
|
|
726
|
+
valueType: "Double",
|
|
727
|
+
annotations: {
|
|
728
|
+
"pl7.app/min": "0",
|
|
729
|
+
"pl7.app/max": "100",
|
|
730
|
+
"pl7.app/table/orderPriority": string(orderDiversityPercents),
|
|
731
|
+
"pl7.app/table/visibility": "default",
|
|
732
|
+
"pl7.app/label": "Refine Tags " + umiTag + " - Output Diversity (%)"
|
|
733
|
+
}
|
|
722
734
|
}
|
|
723
|
-
}
|
|
724
|
-
}
|
|
725
|
-
|
|
735
|
+
}]
|
|
736
|
+
}
|
|
737
|
+
|
|
738
|
+
dataWithUmiColumns = dataWithUmiColumns + [{
|
|
726
739
|
column: "refineTags.numberOfGroupsAccepted",
|
|
727
740
|
id: "refine-tags-number-of-groups-accepted",
|
|
728
741
|
allowNA: true,
|