@platforma-open/milaboratories.mixcr-clonotyping-2.workflow 3.8.2 → 3.10.0

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@3.8.2 build /home/runner/work/mixcr-clonotyping/mixcr-clonotyping/workflow
+> @platforma-open/milaboratories.mixcr-clonotyping-2.workflow@3.10.0 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
 
+## 3.10.0
+
+### Minor Changes
+
+- d2b6d24: fix number of reads, clonotypes, cells in report table
+
+## 3.9.0
+
+### Minor Changes
+
+- 913c474: MILAB-2682: MI_USE_SYSTEM_CA forces MiXCR to trust system installed certificates
+
 ## 3.8.2
 
 ### Patch Changes

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

@@ -600,6 +600,30 @@ getQcReportColumns := func(hasUmi, isSingleCell, sampleIdAxisSpec, chains, cellT
         }
     }]
 
+
+    if !isSingleCell {
+        bulkOrder := 107800
+        for chain in chains {
+            baseColumns = baseColumns + [{
+                column: "clonotypesByChain." + chain,
+                id: "clonotypes-by-chain-" + chain,
+                allowNA: true,
+                naRegex: "NaN",
+                spec: {
+                    name: "mixcr.com/reports/bulk/clonotypesByChain/" + chain,
+                    valueType: "Long",
+                    annotations: {
+                        "pl7.app/min": "0",
+                        "pl7.app/table/orderPriority": string(bulkOrder),
+                        "pl7.app/table/visibility": "default",
+                        "pl7.app/label": "Clonotypes by Chain " + chain
+                    }
+                }
+            }]
+            bulkOrder -= 100
+        }
+    }
+
     dataWithUmiColumns := [    {
         column: "refineTags.UMI.outputCount",
         id: "refine-tags-umi-output-count",
@@ -733,9 +757,51 @@ getQcReportColumns := func(hasUmi, isSingleCell, sampleIdAxisSpec, chains, cellT
         }
     }
     ]
+
+    singleCellColumns := []
     
 
-    singleCellColumns := [
+    singleCellColumns += [{
+        column: "scCellsTotal",
+        id: "sc-cells-total",
+        allowNA: true,
+        naRegex: "NaN",
+        spec: {
+            name: "mixcr.com/reports/singleCell/pairedCellsTotal",
+            valueType: "Long",
+            annotations: {
+                "pl7.app/min": "0",
+                "pl7.app/table/orderPriority": "107900",
+                "pl7.app/table/visibility": "default",
+                "pl7.app/label": "Total number of cells (with paired chains)"
+            }
+        }
+    }]
+
+
+    n := 107800
+    for chain in chains {
+        singleCellColumns += [{
+            column: "clonotypesByChain." + chain,
+            id: "clonotypes-by-chain-" + chain,
+            allowNA: true,
+            naRegex: "NaN",
+            spec: {
+                name: "mixcr.com/reports/singleCell/clonotypesByChain/" + chain,
+                valueType: "Long",
+                annotations: {
+                    "pl7.app/min": "0",
+                    "pl7.app/table/orderPriority": string(n),
+                    "pl7.app/table/visibility": "default",
+                    "pl7.app/label": "Clonotypes by Chain " + chain
+                }
+            }
+        }]
+        n -= 100
+    }
+
+
+    singleCellColumns += [
 
 
 

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@platforma-open/milaboratories.mixcr-clonotyping-2.workflow",
-  "version": "3.8.2",
+  "version": "3.10.0",
   "description": "Tengo-based template",
   "dependencies": {
     "@platforma-sdk/workflow-tengo": "^5.3.3",

package/src/calculate-preset-info.tpl.tengo

@@ -27,6 +27,7 @@ self.body(func(inputs) {
 		inLightQueue().
 		mem("512MiB").
 		software(mixcrSw).
+		env("MI_USE_SYSTEM_CA", "true").
 		secret("MI_LICENSE", "MI_LICENSE").
 		printErrStreamToStdout().
 		arg("exportPreset")
@@ -58,6 +59,7 @@ self.body(func(inputs) {
 		inLightQueue().
 		mem("512MiB").
 		software(mixcrSw).
+		env("MI_USE_SYSTEM_CA", "true").
 		secret("MI_LICENSE", "MI_LICENSE").
 		printErrStreamToStdout().
 		arg("presetSpecificationsForBack").

package/src/export-report.tpl.tengo

@@ -29,10 +29,12 @@ self.body(func(inputs) {
     chains := inputs.chains
     library := inputs.library
     isLibraryFileGzipped := inputs.isLibraryFileGzipped
+    clonotypeTablesData := inputs.clonotypeTablesData
 
     isSingleCell := len(presetSpecForBack.cellTags) > 0
 	hasUmi := !is_undefined(presetSpecForBack.umiTags) && len(presetSpecForBack.umiTags) > 0
     cellTags := presetSpecForBack.cellTags
+    singleCellChainTsvsData := inputs.singleCellChainTsvsData
 
     chainInfos := {
 	"IGHeavy": { mixcrFilter: "IGH", name: "IG Heavy", shortName: "Heavy" },
@@ -55,6 +57,7 @@ self.body(func(inputs) {
     // Build the exportReportsTable command
     exportReportCmd := exec.builder().
         software(mixcrSw).
+        env("MI_USE_SYSTEM_CA", "true").
         secret("MI_LICENSE", "MI_LICENSE").
         arg("exportReportsTable")
     
@@ -96,9 +99,174 @@ self.body(func(inputs) {
         pt.col("fileName").strSlice(0, pt.col("fileName").strLenChars().minus(5)).alias("sampleId")
     )
 
-    // For now, let's just use the processed DataFrame without zero column filtering
-    // since the columns() method is not available in this pTabler version
-    finalDf := processedDf
+    // Calculate real number of exported (productive) clonotypes per sample
+    // Use existing clonotype tables produced earlier; per-sample counts and read sums across chains
+    countDfs := []
+    for chain in chains {
+        chainData := clonotypeTablesData[chain]
+        if is_undefined(chainData) { continue }
+        for key, clonesFile in chainData.inputs() {
+            sampleId := json.decode(key)[0]
+            dfCountSource := wf.frame(clonesFile, { xsvType: "tsv", inferSchema: false, schema: [ { column: "readCount", type: "Double" } ] })
+            dfCount := dfCountSource.select(
+                pt.lit(sampleId).alias("sampleId"),
+                pt.col("clonotypeKey").count().alias("exportedClonotypes"),
+                pt.col("readCount").round().cast("Long").sum().alias("readsUsedInClonotypes")
+            )
+            countDfs = append(countDfs, dfCount)
+        }
+    }
+
+    countsDf := undefined
+    if len(countDfs) > 1 { countsDf = pt.concat(countDfs) } else { countsDf = countDfs[0] }
+    aggregatedCounts := countsDf.groupBy("sampleId").agg(
+        pt.col("exportedClonotypes").sum().alias("exportedClonotypes"),
+        pt.col("readsUsedInClonotypes").sum().alias("readsUsedInClonotypesNew")
+    )
+
+    // Join counts and overwrite totalClonotypes to reflect exported (productive) clones
+    joinedDf := processedDf.join(aggregatedCounts, { how: "left", on: ["sampleId"] })
+
+    // Per-chain clonotype counts
+    perChainJoined := joinedDf
+    for chain in chains {
+        chainData := clonotypeTablesData[chain]
+        chainCol := "clonotypesByChain." + chain
+        if is_undefined(chainData) {
+            perChainJoined = perChainJoined.withColumns(pt.lit(0).alias(chainCol))
+            continue
+        }
+        perChainDfs := []
+        for key, clonesFile in chainData.inputs() {
+            sampleId := json.decode(key)[0]
+            dfSrc := wf.frame(clonesFile, { xsvType: "tsv", inferSchema: false })
+            dfCnt := dfSrc.select(
+                pt.lit(sampleId).alias("sampleId"),
+                pt.col("clonotypeKey").count().alias("__chainCount")
+            )
+            perChainDfs = append(perChainDfs, dfCnt)
+        }
+        if len(perChainDfs) == 0 {
+            perChainJoined = perChainJoined.withColumns(pt.lit(0).alias(chainCol))
+            continue
+        }
+        chainCountsDf := len(perChainDfs) > 1 ? pt.concat(perChainDfs) : perChainDfs[0]
+        chainAgg := chainCountsDf.groupBy("sampleId").agg(
+            pt.col("__chainCount").sum().alias(chainCol)
+        )
+        perChainJoined = perChainJoined.join(chainAgg, { how: "left", on: ["sampleId"] })
+    }
+    // Single-cell: compute per-sample cell pairing stats (both chains vs one chain)
+    if isSingleCell && !is_undefined(singleCellChainTsvsData) {
+        // Expect two chains for receptor; if more, we count any cell having A1 and B1 as both
+        // Build a map of per-sample cellKey presence per chain
+        scDfs := []
+        maps.forEach(singleCellChainTsvsData, func(chainName, chainFiles) {
+            maps.forEach(chainFiles.inputs(), func(key, f) {
+                sampleId := json.decode(key)[0]
+                df := wf.frame(f, { xsvType: "tsv", inferSchema: false, schema: [ { column: "cellKey", type: "String" } ] })
+                df2 := df.select(
+                    pt.lit(sampleId).alias("sampleId"),
+                    pt.col("cellKey").alias("cellKey"),
+                    pt.lit(chainName).alias("chain")
+                )
+                scDfs = append(scDfs, df2)
+            })
+        })
+        if len(scDfs) > 0 {
+            scAll := len(scDfs) > 1 ? pt.concat(scDfs) : scDfs[0]
+            // Count cells per sample across all chains (unique cellKey)
+            cellsPerSample := scAll.groupBy("sampleId").agg(pt.col("cellKey").nUnique().alias("scCellsTotal"))
+
+            // Cells paired across different chains: require the same cellKey to appear in >1 distinct chains per sample
+            cellsPerSampleChainCounts := scAll.groupBy("sampleId", "cellKey").agg(pt.col("chain").nUnique().alias("_numChains"))
+            bothChainCells := cellsPerSampleChainCounts.filter(pt.col("_numChains").gt(1)).groupBy("sampleId").agg(pt.col("cellKey").count().alias("scCellsBothChains"))
+            pairedKeys := cellsPerSampleChainCounts.filter(pt.col("_numChains").gt(1)).select(pt.col("sampleId"), pt.col("cellKey"))
+
+            perChainJoined = perChainJoined.join(cellsPerSample, { how: "left", on: ["sampleId"] })
+            perChainJoined = perChainJoined.join(bothChainCells, { how: "left", on: ["sampleId"] })
+
+            // Recompute per-chain clonotype counts using only paired cells
+            perChainPairedJoined := perChainJoined
+            totalPairedParts := []
+            for chain in chains {
+                chainFiles := singleCellChainTsvsData[chain]
+                chainColPaired := "clonotypesByChain." + chain + ".paired"
+                if is_undefined(chainFiles) {
+                    perChainPairedJoined = perChainPairedJoined.withColumns(pt.lit(0).alias(chainColPaired))
+                    continue
+                }
+                parts := []
+                maps.forEach(chainFiles.inputs(), func(key, f) {
+                    sampleId := json.decode(key)[0]
+                    dfc := wf.frame(f, { xsvType: "tsv", inferSchema: false, schema: [ { column: "cellKey", type: "String" }, { column: "clonotypeKey", type: "String" } ] })
+                    dfc2 := dfc.select(pt.lit(sampleId).alias("sampleId"), pt.col("cellKey"), pt.col("clonotypeKey"))
+                    // join with paired keys for this sample
+                    dfcJoined := dfc2.join(pairedKeys, { how: "inner", on: ["sampleId", "cellKey"] })
+                    parts = append(parts, dfcJoined.select(pt.col("sampleId"), pt.col("clonotypeKey")))
+                })
+                if len(parts) == 0 {
+                    perChainPairedJoined = perChainPairedJoined.withColumns(pt.lit(0).alias(chainColPaired))
+                    continue
+                }
+                partsDf := len(parts) > 1 ? pt.concat(parts) : parts[0]
+                chainAggPaired := partsDf.groupBy("sampleId").agg(pt.col("clonotypeKey").nUnique().alias(chainColPaired))
+                perChainPairedJoined = perChainPairedJoined.join(chainAggPaired, { how: "left", on: ["sampleId"] })
+                totalPairedParts = append(totalPairedParts, chainAggPaired.select(pt.col("sampleId"), pt.col(chainColPaired).alias("__pairedPart")))
+            }
+
+            if len(totalPairedParts) > 0 {
+                totalPairedDf := len(totalPairedParts) > 1 ? pt.concat(totalPairedParts) : totalPairedParts[0]
+                totalPairedAgg := totalPairedDf.groupBy("sampleId").agg(pt.col("__pairedPart").sum().alias("exportedClonotypesPaired"))
+                perChainJoined = perChainPairedJoined.join(totalPairedAgg, { how: "left", on: ["sampleId"] })
+            } else {
+                perChainJoined = perChainPairedJoined.withColumns(pt.lit(0).alias("exportedClonotypesPaired"))
+            }
+        } else {
+            perChainJoined = perChainJoined.withColumns(pt.lit(0).alias("scCellsTotal"), pt.lit(0).alias("scCellsBothChains"))
+        }
+    }
+
+    // Finalize: cast/fill totals and per-chain counts
+    finalDf := perChainJoined
+    if isSingleCell {
+        // Use paired-only totals and per-chain counts
+        // Replace per-chain columns from ".paired" variants and set total from exportedClonotypesPaired
+        for chain in chains {
+            colPaired := "clonotypesByChain." + chain + ".paired"
+            col := "clonotypesByChain." + chain
+            finalDf = finalDf.withColumns(pt.col(colPaired).fillNull(0).cast("Long").alias(col))
+        }
+        finalDf = finalDf.withColumns(
+            pt.col("exportedClonotypesPaired").fillNull(0).cast("Long").alias("totalClonotypes"),
+            pt.col("readsUsedInClonotypesNew").fillNull(0).cast("Long").alias("readsUsedInClonotypes")
+        )
+    } else {
+        finalDf = finalDf.withColumns(
+            pt.col("exportedClonotypes").fillNull(0).cast("Long").alias("totalClonotypes"),
+            pt.col("readsUsedInClonotypesNew").fillNull(0).cast("Long").alias("readsUsedInClonotypes")
+        )
+        for chain in chains {
+            col := "clonotypesByChain." + chain
+            finalDf = finalDf.withColumns(
+                pt.col(col).fillNull(0).cast("Long").alias(col)
+            )
+        }
+    }
+
+    for chain in chains {
+        col := "clonotypesByChain." + chain
+        finalDf = finalDf.withColumns(
+            pt.col(col).fillNull(0).cast("Long").alias(col)
+        )
+    }
+
+    if isSingleCell {
+        // Keep only paired cells count and name it scCellsTotal
+        finalDf = finalDf.withColumns(
+            pt.col("scCellsBothChains").fillNull(0).cast("Long").alias("scCellsTotal")
+        )
+    }
     
     // Save the final DataFrame back to TSV
     finalDf.save("qc-report-processed.tsv", {
@@ -110,7 +278,7 @@ self.body(func(inputs) {
     
     tsvFile := wfResult.getFile("qc-report-processed.tsv")
 
-    qcReportColumns := qcReportColumns(hasUmi, isSingleCell, sampleIdAxisSpec, chainsForMixcr, cellTags)
+    qcReportColumns := qcReportColumns(hasUmi, isSingleCell, sampleIdAxisSpec, chains, cellTags)
     reportColumnsSpec := qcReportColumns.reportColumnsSpec
 
     qcReportTable := xsv.importFile(

package/src/list-presets.tpl.tengo

@@ -17,6 +17,7 @@ self.body(func(inputs) {
 		cpu(1).
 		mem("512MiB").
 		software(mixcrSw).
+		env("MI_USE_SYSTEM_CA", "true").
 		secret("MI_LICENSE", "MI_LICENSE").
 		arg("listPresetSpecificationsForUI").
 		arg("presets.json").

package/src/mixcr-analyze.tpl.tengo

@@ -66,6 +66,7 @@ self.body(func(inputs) {
 
 	mixcrCmdBuilder := exec.builder().
 		printErrStreamToStdout().
+		env("MI_USE_SYSTEM_CA", "true").
 		env("MI_PROGRESS_PREFIX", progressPrefix).
 		software(mixcrSw).
 		secret("MI_LICENSE", "MI_LICENSE").

package/src/mixcr-export.tpl.tengo

@@ -54,6 +54,7 @@ self.body(func(inputs) {
 		    cpu(2).
 			printErrStreamToStdout().
 			dontSaveStdoutOrStderr().
+			env("MI_USE_SYSTEM_CA", "true").
 			software(mixcrSw).
 			secret("MI_LICENSE", "MI_LICENSE").
 			arg("exportClones").

package/src/process.tpl.tengo

@@ -319,7 +319,9 @@ self.body(func(inputs) {
 		return schema
 	}
 
-	clonotypeTables := pframes.pFrameBuilder()
+    clonotypeTables := pframes.pFrameBuilder()
+    singleCellChainTsvs := {}
+    clonotypeTablesData := {}
 	resultsToCache := {}
 
 	for chain in chains {
@@ -456,8 +458,9 @@ self.body(func(inputs) {
 			} ]
 		}
 
-		resultsToCache["clonotypeTable/" + chain] = exportResults.outputData("clonotypeTable")
-		clonotypeTables.add(chain, exportResults.outputSpec("clonotypeTable"), exportResults.outputData("clonotypeTable"))
+        resultsToCache["clonotypeTable/" + chain] = exportResults.outputData("clonotypeTable")
+        clonotypeTablesData[chain] = exportResults.outputData("clonotypeTable")
+        clonotypeTables.add(chain, exportResults.outputSpec("clonotypeTable"), exportResults.outputData("clonotypeTable"))
 
 		aggregateByCloneKey := pframes.processColumn(
 			exportResults.output("clonotypeTable"),
@@ -485,7 +488,7 @@ self.body(func(inputs) {
 			}
 		)
 
-		if isSingleCell {
+        if isSingleCell {
 			// collecting results for future single cell processing
 			perChainResults[chain] = {
 				tsvForSingleCell: exportResults.output("clonotypeTableForSingleCell"),
@@ -495,6 +498,9 @@ self.body(func(inputs) {
 			// caching intermediate results until the block is removed
 			resultsToCache["clonotypeTableForSingleCell/" + chain] = exportResults.outputData("clonotypeTableForSingleCell")
 			resultsToCache["clonotypeProperties/" + chain] = aggregateByCloneKey.outputData("clonotypeProperties")
+
+            // collect per-chain single-cell TSVs for QC report stats
+            singleCellChainTsvs[chain] = exportResults.outputData("clonotypeTableForSingleCell")
 		} else {
 			// only adding data outputs if we are in bulk mode
 			exportResults.addXsvOutputToBuilder(clonotypes, "byCloneKeyBySample", "byCloneKeyBySample/" + chain + "/")
@@ -693,13 +699,15 @@ self.body(func(inputs) {
 		}
 	}
 
-	qcReportTable := render.create(exportReportTpl, {
+    qcReportTable := render.create(exportReportTpl, {
 		clnsData: mixcrResults.outputData("clns"),
 		presetSpecForBack: presetSpecForBack,
 		sampleIdAxisSpec: sampleIdAxisSpec,
-		chains: chains,
+        chains: chains,
 		library: library,
-		isLibraryFileGzipped: isLibraryFileGzipped
+		isLibraryFileGzipped: isLibraryFileGzipped,
+        clonotypeTablesData: clonotypeTablesData,
+		singleCellChainTsvsData: singleCellChainTsvs
 	})
 
 	return {

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

@@ -600,6 +600,30 @@ getQcReportColumns := func(hasUmi, isSingleCell, sampleIdAxisSpec, chains, cellT
         }
     }]
 
+    // Add per-chain clonotype counts for bulk datasets (avoid duplicates in single-cell)
+    if !isSingleCell {
+        bulkOrder := 107800
+        for chain in chains {
+            baseColumns = baseColumns + [{
+                column: "clonotypesByChain." + chain,
+                id: "clonotypes-by-chain-" + chain,
+                allowNA: true,
+                naRegex: "NaN",
+                spec: {
+                    name: "mixcr.com/reports/bulk/clonotypesByChain/" + chain,
+                    valueType: "Long",
+                    annotations: {
+                        "pl7.app/min": "0",
+                        "pl7.app/table/orderPriority": string(bulkOrder),
+                        "pl7.app/table/visibility": "default",
+                        "pl7.app/label": "Clonotypes by Chain " + chain
+                    }
+                }
+            }]
+            bulkOrder -= 100
+        }
+    }
+
     dataWithUmiColumns := [    {
         column: "refineTags.UMI.outputCount",
         id: "refine-tags-umi-output-count",
@@ -733,9 +757,51 @@ getQcReportColumns := func(hasUmi, isSingleCell, sampleIdAxisSpec, chains, cellT
         }
     }
     ]
+
+    singleCellColumns := []
     
+    // Paired cells total (single-cell): number of cells with distinct chains per sample
+    singleCellColumns += [{
+        column: "scCellsTotal",
+        id: "sc-cells-total",
+        allowNA: true,
+        naRegex: "NaN",
+        spec: {
+            name: "mixcr.com/reports/singleCell/pairedCellsTotal",
+            valueType: "Long",
+            annotations: {
+                "pl7.app/min": "0",
+                "pl7.app/table/orderPriority": "107900",
+                "pl7.app/table/visibility": "default",
+                "pl7.app/label": "Total number of cells (with paired chains)"
+            }
+        }
+    }]
+
+    // Per-chain clonotype counts (paired-only in single-cell), one column per available chain
+    n := 107800
+    for chain in chains {
+        singleCellColumns += [{
+            column: "clonotypesByChain." + chain,
+            id: "clonotypes-by-chain-" + chain,
+            allowNA: true,
+            naRegex: "NaN",
+            spec: {
+                name: "mixcr.com/reports/singleCell/clonotypesByChain/" + chain,
+                valueType: "Long",
+                annotations: {
+                    "pl7.app/min": "0",
+                    "pl7.app/table/orderPriority": string(n),
+                    "pl7.app/table/visibility": "default",
+                    "pl7.app/label": "Clonotypes by Chain " + chain
+                }
+            }
+        }]
+        n -= 100
+    }
+
     // Single Cell columns
-    singleCellColumns := [
+    singleCellColumns += [
     // {
     //     column: "align.readsWithChain.IGH",
     //     id: "align-reads-with-chain-igh",