@platforma-open/milaboratories.mixcr-clonotyping-2.workflow 3.2.0 → 3.3.0

package/.turbo/turbo-build.log

@@ -1,6 +1,6 @@
  WARN  Issue while reading "/home/runner/work/mixcr-clonotyping/mixcr-clonotyping/.npmrc". Failed to replace env in config: ${NPMJS_TOKEN}
 
-> @platforma-open/milaboratories.mixcr-clonotyping-2.workflow@3.2.0 build /home/runner/work/mixcr-clonotyping/mixcr-clonotyping/workflow
+> @platforma-open/milaboratories.mixcr-clonotyping-2.workflow@3.3.0 build /home/runner/work/mixcr-clonotyping/mixcr-clonotyping/workflow
 > rm -rf dist && pl-tengo check && pl-tengo build
 
   info: Skipping unknown file type: test/columns.test.ts

package/CHANGELOG.md

@@ -1,5 +1,17 @@
 # @platforma-open/milaboratories.mixcr-clonotyping.workflow
 
+## 3.3.0
+
+### Minor Changes
+
+- 8cee126: min quality columns added
+
+## 3.2.1
+
+### Patch Changes
+
+- ebad6c6: Fixes export error on SC presets without UMI
+
 ## 3.2.0
 
 ### Minor Changes

package/dist/tengo/lib/calculate-export-specs.lib.tengo

@@ -467,6 +467,27 @@ calculateExportSpecs := func(presetSpecForBack, sampleIdAxisSpec, blockId) {
 						}
 					} ]
 				exportArgs += [ [ "-" + alphabetShortMixcr + "Feature" + imputedU, featureInFrameU ] ]
+				if !isImputed && !isAminoAcid {
+					columnsSpecPerClonotypeNoAggregates += [ {
+							column: "minQual" + featureU,
+							id: "min-qual-" + featureL,
+							naRegex: "region_not_covered",
+							spec: {
+								name: "pl7.app/vdj/sequenceQuality",
+								valueType: "Int",
+								domain: {
+									"pl7.app/vdj/quality": "minQuality",
+									"pl7.app/vdj/feature": featureU
+								},
+								annotations: a(orderP - 10, false, {
+									"pl7.app/min": "0",
+									"pl7.app/max": "60",
+									"pl7.app/label": "Min quality " + featureU
+								})
+							}
+						} ]
+					exportArgs += [ [ "-minFeatureQuality", featureU ] ]
+				}
 				orderP -= 100
 
 

package/dist/tengo/lib/qc-report-columns.lib.tengo

@@ -5,7 +5,7 @@ ll := import("@platforma-sdk/workflow-tengo:ll")
 pConstants := import("@platforma-sdk/workflow-tengo:pframes.constants")
 
 
-getQcReportColumns := func(hasUmi, isSingleCell, sampleIdAxisSpec, chains) {
+getQcReportColumns := func(hasUmi, isSingleCell, sampleIdAxisSpec, chains, cellTags) {
 
     baseColumns := [
     {
@@ -489,7 +489,7 @@ getQcReportColumns := func(hasUmi, isSingleCell, sampleIdAxisSpec, chains) {
         column: "assemble.preCloneAssembler.unassignedAlignments",
         id: "assemble-pre-clone-assembler-unassigned-alignments",
         allowNA: true,
-        naRegex: "",
+        naRegex: "^[a-zA-Z_]*$",
         spec: {
             name: "mixcr.com/reports/assemble/preCloneAssembler/unassignedAlignments",
             valueType: "Long",
@@ -505,7 +505,7 @@ getQcReportColumns := func(hasUmi, isSingleCell, sampleIdAxisSpec, chains) {
         column: "assemble.preCloneAssembler.unassignedAlignmentsPercents",
         id: "assemble-pre-clone-assembler-unassigned-alignments-percents",
         allowNA: true,
-        naRegex: "",
+        naRegex: "^[a-zA-Z_]*$",
         spec: {
             name: "mixcr.com/reports/assemble/preCloneAssembler/unassignedAlignmentsPercents",
             valueType: "Double",
@@ -1180,73 +1180,76 @@ getQcReportColumns := func(hasUmi, isSingleCell, sampleIdAxisSpec, chains) {
                 "pl7.app/label": "Unassigned Clonotypes (%)"
             }
         }
-    },
-    {
-        column: "refineTags.CELL.outputCount",
-        id: "refine-tags-cell-output-count",
-        allowNA: true,
-        naRegex: "NaN",
-        spec: {
-            name: "mixcr.com/reports/refineTags/CELL/outputCount",
-            valueType: "Long",
-            annotations: {
-                "pl7.app/min": "0",
-                "pl7.app/table/orderPriority": "85800",
-                "pl7.app/table/visibility": "optional",
-                "pl7.app/label": "Refine Tags CELL - Output Count"
+    }]
+
+    for cellTag in cellTags {
+        singleCellColumns += [{
+            column: "refineTags." + cellTag + ".outputCount",
+            id: "refine-tags-" + cellTag + "-output-count",
+            allowNA: true,
+            naRegex: "NaN",
+            spec: {
+                name: "mixcr.com/reports/refineTags/CELL/outputCount",
+                valueType: "Long",
+                annotations: {
+                    "pl7.app/min": "0",
+                    "pl7.app/table/orderPriority": "85800",
+                    "pl7.app/table/visibility": "optional",
+                    "pl7.app/label": "Refine Tags " + cellTag + " - Output Count"
+                }
             }
-        }
-    },
-    {
-        column: "refineTags.CELL.outputCountPercents",
-        id: "refine-tags-cell-output-count-percents",
-        allowNA: true,
-        naRegex: "NaN",
-        spec: {
-            name: "mixcr.com/reports/refineTags/CELL/outputCountPercents",
-            valueType: "Double",
-            annotations: {
-                "pl7.app/min": "0",
-                "pl7.app/max": "100",
-                "pl7.app/table/orderPriority": "85900",
-                "pl7.app/table/visibility": "default",
-                "pl7.app/label": "Refine Tags CELL - Output Count (%)"
+        },
+        {
+            column: "refineTags." + cellTag + ".outputCountPercents",
+            id: "refine-tags-" + cellTag + "-output-count-percents",
+            allowNA: true,
+            naRegex: "NaN",
+            spec: {
+                name: "mixcr.com/reports/refineTags/CELL/outputCountPercents",
+                valueType: "Double",
+                annotations: {
+                    "pl7.app/min": "0",
+                    "pl7.app/max": "100",
+                    "pl7.app/table/orderPriority": "85900",
+                    "pl7.app/table/visibility": "default",
+                    "pl7.app/label": "Refine Tags " + cellTag + " - Output Count (%)"
+                }
             }
-        }
-    },
-    {
-        column: "refineTags.CELL.outputDiversity",
-        id: "refine-tags-cell-output-diversity",
-        allowNA: true,
-        naRegex: "NaN",
-        spec: {
-            name: "mixcr.com/reports/refineTags/CELL/outputDiversity",
-            valueType: "Long",
-            annotations: {
-                "pl7.app/min": "0",
-                "pl7.app/table/orderPriority": "86000",
-                "pl7.app/table/visibility": "optional",
-                "pl7.app/label": "Refine Tags CELL - Output Diversity"
+        },
+        {
+            column: "refineTags." + cellTag + ".outputDiversity",
+            id: "refine-tags-" + cellTag + "-output-diversity",
+            allowNA: true,
+            naRegex: "NaN",
+            spec: {
+                name: "mixcr.com/reports/refineTags/CELL/outputDiversity",
+                valueType: "Long",
+                annotations: {
+                    "pl7.app/min": "0",
+                    "pl7.app/table/orderPriority": "86000",
+                    "pl7.app/table/visibility": "optional",
+                    "pl7.app/label": "Refine Tags " + cellTag + " - Output Diversity"
+                }
             }
-        }
-    },
-    {
-        column: "refineTags.CELL.outputDiversityPercents",
-        id: "refine-tags-cell-output-diversity-percents",
-        allowNA: true,
-        naRegex: "NaN",
-        spec: {
-            name: "mixcr.com/reports/refineTags/CELL/outputDiversityPercents",
-            valueType: "Double",
-            annotations: {
-                "pl7.app/min": "0",
-                "pl7.app/max": "100",
-                "pl7.app/table/orderPriority": "86100",
-                "pl7.app/table/visibility": "default",
-                "pl7.app/label": "Refine Tags CELL - Output Diversity (%)"
+        },
+        {
+            column: "refineTags." + cellTag + ".outputDiversityPercents",
+            id: "refine-tags-" + cellTag + "-output-diversity-percents",
+            allowNA: true,
+            naRegex: "NaN",
+            spec: {
+                name: "mixcr.com/reports/refineTags/CELL/outputDiversityPercents",
+                valueType: "Double",
+                annotations: {
+                    "pl7.app/min": "0",
+                    "pl7.app/max": "100",
+                    "pl7.app/table/orderPriority": "86100",
+                    "pl7.app/table/visibility": "default",
+                    "pl7.app/label": "Refine Tags " + cellTag + " - Output Diversity (%)"
+                }
             }
-        }
-    }]
+        }]
+    }
 
 
 

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@platforma-open/milaboratories.mixcr-clonotyping-2.workflow",
-  "version": "3.2.0",
+  "version": "3.3.0",
   "description": "Tengo-based template",
   "dependencies": {
     "@platforma-sdk/workflow-tengo": "^5.0.3",

package/src/aggregate-by-clonotype-key.tpl.tengo

@@ -41,7 +41,7 @@ self.body(func(inputs) {
 
 	baseSchemaForRead := schemaPerSample + [ { column: "clonotypeKey", type: "String" } ]
 
-	ll.print("__THE_LOG__ AGGREGATE BY CLONOTYPE KEY: " + json.encode(maps.getKeys(inputMap)))
+	// ll.print("__THE_LOG__ AGGREGATE BY CLONOTYPE KEY: " + json.encode(maps.getKeys(inputMap)))
 
 	for sKey in maps.getKeys(inputMap) {
 		inputFile := inputMap[sKey]

package/src/calculate-export-specs.lib.tengo

@@ -467,6 +467,27 @@ calculateExportSpecs := func(presetSpecForBack, sampleIdAxisSpec, blockId) {
 						}
 					} ]
 				exportArgs += [ [ "-" + alphabetShortMixcr + "Feature" + imputedU, featureInFrameU ] ]
+				if !isImputed && !isAminoAcid {
+					columnsSpecPerClonotypeNoAggregates += [ {
+							column: "minQual" + featureU,
+							id: "min-qual-" + featureL,
+							naRegex: "region_not_covered",
+							spec: {
+								name: "pl7.app/vdj/sequenceQuality",
+								valueType: "Int",
+								domain: {
+									"pl7.app/vdj/quality": "minQuality",
+									"pl7.app/vdj/feature": featureU
+								},
+								annotations: a(orderP - 10, false, {
+									"pl7.app/min": "0",
+									"pl7.app/max": "60",
+									"pl7.app/label": "Min quality " + featureU
+								})
+							}
+						} ]
+					exportArgs += [ [ "-minFeatureQuality", featureU ] ]
+				}
 				orderP -= 100
 
 				// Adding sequence annotation columns for assembling feature

package/src/export-report.tpl.tengo

@@ -24,11 +24,14 @@ ptablerSw := assets.importSoftware("@platforma-open/milaboratories.software-ptab
 
 self.body(func(inputs) {
     clnsData := inputs.clnsData
-    isSingleCell := inputs.isSingleCell
-    hasUmi := inputs.hasUmi
+    presetSpecForBack := inputs.presetSpecForBack
     sampleIdAxisSpec := inputs.sampleIdAxisSpec
     chains := inputs.chains
 
+    isSingleCell := len(presetSpecForBack.cellTags) > 0
+	hasUmi := !is_undefined(presetSpecForBack.umiTags) && len(presetSpecForBack.umiTags) > 0
+    cellTags := presetSpecForBack.cellTags
+
     chainInfos := {
 	"IGHeavy": { mixcrFilter: "IGH", name: "IG Heavy", shortName: "Heavy" },
 	"IGLight": { mixcrFilter: "IGK,IGL", name: "IG Light", shortName: "Light" },
@@ -98,7 +101,7 @@ self.body(func(inputs) {
     
     tsvFile := wfResult.getFile("qc-report-processed.tsv")
 
-    qcReportColumns := qcReportColumns(hasUmi, isSingleCell, sampleIdAxisSpec, chainsForMixcr)
+    qcReportColumns := qcReportColumns(hasUmi, isSingleCell, sampleIdAxisSpec, chainsForMixcr, cellTags)
     reportColumnsSpec := qcReportColumns.reportColumnsSpec
 
     qcReportTable := xsv.importFile(

package/src/mixcr-export.tpl.tengo

@@ -35,6 +35,7 @@ self.body(func(inputs) {
 	}
 
 	mainAbundanceColumnUnnormalizedArgs := params.mainAbundanceColumnUnnormalizedArgs
+	mainAbundanceColumnIsReadCount := params.mainAbundanceColumnIsReadCount == true
 	mainIsProductiveArgs := params.mainIsProductiveArgs
 
 	hashKeyDerivationExpressionPt := func(sourceColumns) {
@@ -145,7 +146,22 @@ self.body(func(inputs) {
 			mem("4GiB").
 			cpu(2)
 
-		dfSingleCell := wfSingleCell.frame(unprocessedTsvForSingleCell, { xsvType: "tsv", inferSchema: false })
+		frameLoadOps := {
+			xsvType: "tsv",
+			inferSchema: false
+		}
+
+		if mainAbundanceColumnIsReadCount {
+			frameLoadOps.schema = [ { column: "readCount", type: "Double" } ]
+		}
+
+		dfSingleCell := wfSingleCell.frame(unprocessedTsvForSingleCell, frameLoadOps)
+
+		if mainAbundanceColumnIsReadCount {
+			dfSingleCell.addColumns(
+				pt.col("readCount").round().cast("Long").alias("readCount")
+			)
+		}
 
 		dfSingleCell.addColumns(
 			hashKeyDerivationExpressionPt(clonotypeKeyColumns).alias("clonotypeKey"),

package/src/process-single-cell.tpl.tengo

@@ -22,7 +22,7 @@ self.defineOutputs("abundanceTsv", "clonotypeTsv",
 ptablerSw := assets.importSoftware("@platforma-open/milaboratories.software-ptabler:main")
 
 self.body(func(inputs) {
-	ll.print("__THE_LOG__ PROCESS SINGLE CELL")
+	// ll.print("__THE_LOG__ PROCESS SINGLE CELL")
 
 	byCellTagA := inputs[pConstants.VALUE_FIELD_NAME]
 	inputDataMeta := byCellTagA.getDataAsJson()

package/src/process.tpl.tengo

@@ -391,7 +391,7 @@ self.body(func(inputs) {
 				stepCache: 30 * times.minute,
 
 				extra: {
-					params: {
+					params: maps.clone({
 						chains: chainInfo.mixcrFilter,
 						clonotypeKeyColumns: clonotypeKeyColumns,
 						clonotypeKeyArgs: clonotypeKeyArgs,
@@ -406,9 +406,11 @@ self.body(func(inputs) {
 						cellTagColumns: cellTagColumns,
 						hashCellKey: hashCellKey,
 
+						mainAbundanceColumnIsReadCount: (!is_undefined(cellTagColumns) && len(cellTagColumns) > 0 && mainAbundanceColumnUnnormalized == "readCount") ? true : undefined,
+
 						exportArgs: exportArgs,
 						isLibraryFileGzipped: isLibraryFileGzipped
-					},
+					}, { removeUndefs: true }),
 					library: library
 				}
 			}
@@ -683,14 +685,13 @@ self.body(func(inputs) {
 					anonymize.deanonymizePKeys(anonymizedData, 0, [0], anonymizationResult.mapping)
 				)
 				resultsToCache["clonotypeProperties/" + receptor + "/cellsLinkerTable/" + columnName] = anonymizedData
-			}		
+			}
 		}
 	}
 
 	qcReportTable := render.create(exportReportTpl, {
 		clnsData: mixcrResults.outputData("clns"),
-		isSingleCell: isSingleCell,
-		hasUmi: hasUmi,
+		presetSpecForBack: presetSpecForBack,
 		sampleIdAxisSpec: sampleIdAxisSpec,
 		chains: chains
 	})

package/src/qc-report-columns.lib.tengo

@@ -5,7 +5,7 @@ ll := import("@platforma-sdk/workflow-tengo:ll")
 pConstants := import("@platforma-sdk/workflow-tengo:pframes.constants")
 
 // QC Report column specifications function
-getQcReportColumns := func(hasUmi, isSingleCell, sampleIdAxisSpec, chains) {
+getQcReportColumns := func(hasUmi, isSingleCell, sampleIdAxisSpec, chains, cellTags) {
     // Bulk sequencing columns
     baseColumns := [
     {
@@ -489,7 +489,7 @@ getQcReportColumns := func(hasUmi, isSingleCell, sampleIdAxisSpec, chains) {
         column: "assemble.preCloneAssembler.unassignedAlignments",
         id: "assemble-pre-clone-assembler-unassigned-alignments",
         allowNA: true,
-        naRegex: "",
+        naRegex: "^[a-zA-Z_]*$",
         spec: {
             name: "mixcr.com/reports/assemble/preCloneAssembler/unassignedAlignments",
             valueType: "Long",
@@ -505,7 +505,7 @@ getQcReportColumns := func(hasUmi, isSingleCell, sampleIdAxisSpec, chains) {
         column: "assemble.preCloneAssembler.unassignedAlignmentsPercents",
         id: "assemble-pre-clone-assembler-unassigned-alignments-percents",
         allowNA: true,
-        naRegex: "",
+        naRegex: "^[a-zA-Z_]*$",
         spec: {
             name: "mixcr.com/reports/assemble/preCloneAssembler/unassignedAlignmentsPercents",
             valueType: "Double",
@@ -1180,73 +1180,76 @@ getQcReportColumns := func(hasUmi, isSingleCell, sampleIdAxisSpec, chains) {
                 "pl7.app/label": "Unassigned Clonotypes (%)"
             }
         }
-    },
-    {
-        column: "refineTags.CELL.outputCount",
-        id: "refine-tags-cell-output-count",
-        allowNA: true,
-        naRegex: "NaN",
-        spec: {
-            name: "mixcr.com/reports/refineTags/CELL/outputCount",
-            valueType: "Long",
-            annotations: {
-                "pl7.app/min": "0",
-                "pl7.app/table/orderPriority": "85800",
-                "pl7.app/table/visibility": "optional",
-                "pl7.app/label": "Refine Tags CELL - Output Count"
+    }]
+
+    for cellTag in cellTags {
+        singleCellColumns += [{
+            column: "refineTags." + cellTag + ".outputCount",
+            id: "refine-tags-" + cellTag + "-output-count",
+            allowNA: true,
+            naRegex: "NaN",
+            spec: {
+                name: "mixcr.com/reports/refineTags/CELL/outputCount",
+                valueType: "Long",
+                annotations: {
+                    "pl7.app/min": "0",
+                    "pl7.app/table/orderPriority": "85800",
+                    "pl7.app/table/visibility": "optional",
+                    "pl7.app/label": "Refine Tags " + cellTag + " - Output Count"
+                }
             }
-        }
-    },
-    {
-        column: "refineTags.CELL.outputCountPercents",
-        id: "refine-tags-cell-output-count-percents",
-        allowNA: true,
-        naRegex: "NaN",
-        spec: {
-            name: "mixcr.com/reports/refineTags/CELL/outputCountPercents",
-            valueType: "Double",
-            annotations: {
-                "pl7.app/min": "0",
-                "pl7.app/max": "100",
-                "pl7.app/table/orderPriority": "85900",
-                "pl7.app/table/visibility": "default",
-                "pl7.app/label": "Refine Tags CELL - Output Count (%)"
+        },
+        {
+            column: "refineTags." + cellTag + ".outputCountPercents",
+            id: "refine-tags-" + cellTag + "-output-count-percents",
+            allowNA: true,
+            naRegex: "NaN",
+            spec: {
+                name: "mixcr.com/reports/refineTags/CELL/outputCountPercents",
+                valueType: "Double",
+                annotations: {
+                    "pl7.app/min": "0",
+                    "pl7.app/max": "100",
+                    "pl7.app/table/orderPriority": "85900",
+                    "pl7.app/table/visibility": "default",
+                    "pl7.app/label": "Refine Tags " + cellTag + " - Output Count (%)"
+                }
             }
-        }
-    },
-    {
-        column: "refineTags.CELL.outputDiversity",
-        id: "refine-tags-cell-output-diversity",
-        allowNA: true,
-        naRegex: "NaN",
-        spec: {
-            name: "mixcr.com/reports/refineTags/CELL/outputDiversity",
-            valueType: "Long",
-            annotations: {
-                "pl7.app/min": "0",
-                "pl7.app/table/orderPriority": "86000",
-                "pl7.app/table/visibility": "optional",
-                "pl7.app/label": "Refine Tags CELL - Output Diversity"
+        },
+        {
+            column: "refineTags." + cellTag + ".outputDiversity",
+            id: "refine-tags-" + cellTag + "-output-diversity",
+            allowNA: true,
+            naRegex: "NaN",
+            spec: {
+                name: "mixcr.com/reports/refineTags/CELL/outputDiversity",
+                valueType: "Long",
+                annotations: {
+                    "pl7.app/min": "0",
+                    "pl7.app/table/orderPriority": "86000",
+                    "pl7.app/table/visibility": "optional",
+                    "pl7.app/label": "Refine Tags " + cellTag + " - Output Diversity"
+                }
             }
-        }
-    },
-    {
-        column: "refineTags.CELL.outputDiversityPercents",
-        id: "refine-tags-cell-output-diversity-percents",
-        allowNA: true,
-        naRegex: "NaN",
-        spec: {
-            name: "mixcr.com/reports/refineTags/CELL/outputDiversityPercents",
-            valueType: "Double",
-            annotations: {
-                "pl7.app/min": "0",
-                "pl7.app/max": "100",
-                "pl7.app/table/orderPriority": "86100",
-                "pl7.app/table/visibility": "default",
-                "pl7.app/label": "Refine Tags CELL - Output Diversity (%)"
+        },
+        {
+            column: "refineTags." + cellTag + ".outputDiversityPercents",
+            id: "refine-tags-" + cellTag + "-output-diversity-percents",
+            allowNA: true,
+            naRegex: "NaN",
+            spec: {
+                name: "mixcr.com/reports/refineTags/CELL/outputDiversityPercents",
+                valueType: "Double",
+                annotations: {
+                    "pl7.app/min": "0",
+                    "pl7.app/max": "100",
+                    "pl7.app/table/orderPriority": "86100",
+                    "pl7.app/table/visibility": "default",
+                    "pl7.app/label": "Refine Tags " + cellTag + " - Output Diversity (%)"
+                }
             }
-        }
-    }]
+        }]
+    }
 
     // for chain in chains {
     //     singleCellColumns += [{