@platforma-open/milaboratories.mixcr-clonotyping-2.workflow 3.1.1 → 3.2.1

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@3.1.1 build /home/runner/work/mixcr-clonotyping/mixcr-clonotyping/workflow
+> @platforma-open/milaboratories.mixcr-clonotyping-2.workflow@3.2.1 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
 
+## 3.2.1
+
+### Patch Changes
+
+- ebad6c6: Fixes export error on SC presets without UMI
+
+## 3.2.0
+
+### Minor Changes
+
+- 73af94c: nLengthTotalAdded column NA regex fix
+
 ## 3.1.1
 
 ### Patch Changes

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

@@ -545,12 +545,11 @@ calculateExportSpecs := func(presetSpecForBack, sampleIdAxisSpec, blockId) {
 	junctionTypes := [ "VJ", "VD", "DJ" ]
 	for junctionType in junctionTypes {
 		feature := junctionType + "Junction"
-		naRegex := junctionType == "VJ" ? "region_not_covered" : "no_d_gene"
 
 		columnsSpecPerClonotypeNoAggregates += [ {
 			column: "nLength" + feature,
 			id: "n-length-" + text.to_lower(junctionType) + "-junction",
-			naRegex: naRegex,
+			naRegex: "^[a-z_]*$",
 			allowNA: true,
 			spec: {
 				name: "pl7.app/vdj/sequenceLength",
@@ -572,7 +571,7 @@ calculateExportSpecs := func(presetSpecForBack, sampleIdAxisSpec, blockId) {
 	columnsSpecPerClonotypeNoAggregates += [ {
 		column: "nLengthTotalAdded",
 		id: "n-length-total-added",
-		naRegex: "region_not_covered|no_d_gene",
+		naRegex: "^[a-z_]*$",
 		allowNA: true,
 		spec: {
 			name: "pl7.app/vdj/sequenceLength",

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",
@@ -736,204 +736,204 @@ getQcReportColumns := func(hasUmi, isSingleCell, sampleIdAxisSpec, chains) {
     
 
     singleCellColumns := [
-    {
-        column: "align.readsWithChain.IGH",
-        id: "align-reads-with-chain-igh",
-        allowNA: true,
-        naRegex: "",
-        spec: {
-            name: "mixcr.com/reports/align/readsWithChain/IGH",
-            valueType: "Long",
-            annotations: {
-                "pl7.app/min": "0",
-                "pl7.app/table/orderPriority": "96000",
-                "pl7.app/table/visibility": "optional",
-                "pl7.app/label": "Reads with Chain IGH"
-            }
-        }
-    },
-    {
-        column: "align.readsWithChain.IGHPercents",
-        id: "align-reads-with-chain-igh-percents",
-        allowNA: true,
-        naRegex: "",
-        spec: {
-            name: "mixcr.com/reports/align/readsWithChain/IGHPercents",
-            valueType: "Double",
-            annotations: {
-                "pl7.app/min": "0",
-                "pl7.app/max": "100",
-                "pl7.app/table/orderPriority": "96100",
-                "pl7.app/table/visibility": "default",
-                "pl7.app/label": "Reads with Chain IGH (%)"
-            }
-        }
-    },
-    {
-        column: "align.readsWithChain.IGK",
-        id: "align-reads-with-chain-igk",
-        allowNA: true,
-        naRegex: "",
-        spec: {
-            name: "mixcr.com/reports/align/readsWithChain/IGK",
-            valueType: "Long",
-            annotations: {
-                "pl7.app/min": "0",
-                "pl7.app/table/orderPriority": "96200",
-                "pl7.app/table/visibility": "optional",
-                "pl7.app/label": "Reads with Chain IGK"
-            }
-        }
-    },
-    {
-        column: "align.readsWithChain.IGKPercents",
-        id: "align-reads-with-chain-igk-percents",
-        allowNA: true,
-        naRegex: "",
-        spec: {
-            name: "mixcr.com/reports/align/readsWithChain/IGKPercents",
-            valueType: "Double",
-            annotations: {
-                "pl7.app/min": "0",
-                "pl7.app/max": "100",
-                "pl7.app/table/orderPriority": "96300",
-                "pl7.app/table/visibility": "default",
-                "pl7.app/label": "Reads with Chain IGK (%)"
-            }
-        }
-    },
-    {
-        column: "align.readsWithChain.IGL",
-        id: "align-reads-with-chain-igl",
-        allowNA: true,
-        naRegex: "",
-        spec: {
-            name: "mixcr.com/reports/align/readsWithChain/IGL",
-            valueType: "Long",
-            annotations: {
-                "pl7.app/min": "0",
-                "pl7.app/table/orderPriority": "96400",
-                "pl7.app/table/visibility": "optional",
-                "pl7.app/label": "Reads with Chain IGL"
-            }
-        }
-    },
-    {
-        column: "align.readsWithChain.IGLPercents",
-        id: "align-reads-with-chain-igl-percents",
-        allowNA: true,
-        naRegex: "",
-        spec: {
-            name: "mixcr.com/reports/align/readsWithChain/IGLPercents",
-            valueType: "Double",
-            annotations: {
-                "pl7.app/min": "0",
-                "pl7.app/max": "100",
-                "pl7.app/table/orderPriority": "96500",
-                "pl7.app/table/visibility": "default",
-                "pl7.app/label": "Reads with Chain IGL (%)"
-            }
-        }
-    },
-    {
-        column: "align.readsWithChain.TRAD",
-        id: "align-reads-with-chain-trad",
-        allowNA: true,
-        naRegex: "",
-        spec: {
-            name: "mixcr.com/reports/align/readsWithChain/TRAD",
-            valueType: "Long",
-            annotations: {
-                "pl7.app/min": "0",
-                "pl7.app/table/orderPriority": "96700",
-                "pl7.app/table/visibility": "optional",
-                "pl7.app/label": "Reads with Chain TRAD"
-            }
-        }
-    },
-    {
-        column: "align.readsWithChain.TRADPercents",
-        id: "align-reads-with-chain-trad-percents",
-        allowNA: true,
-        naRegex: "",
-        spec: {
-            name: "mixcr.com/reports/align/readsWithChain/TRADPercents",
-            valueType: "Double",
-            annotations: {
-                "pl7.app/min": "0",
-                "pl7.app/max": "100",
-                "pl7.app/table/orderPriority": "96800",
-                "pl7.app/table/visibility": "default",
-                "pl7.app/label": "Reads with Chain TRAD (%)"
-            }
-        }
-    },
-    {
-        column: "align.readsWithChain.TRB",
-        id: "align-reads-with-chain-trb",
-        allowNA: true,
-        naRegex: "",
-        spec: {
-            name: "mixcr.com/reports/align/readsWithChain/TRB",
-            valueType: "Long",
-            annotations: {
-                "pl7.app/min": "0",
-                "pl7.app/table/orderPriority": "97000",
-                "pl7.app/table/visibility": "optional",
-                "pl7.app/label": "Reads with Chain TRB"
-            }
-        }
-    },
-    {
-        column: "align.readsWithChain.TRBPercents",
-        id: "align-reads-with-chain-trb-percents",
-        allowNA: true,
-        naRegex: "",
-        spec: {
-            name: "mixcr.com/reports/align/readsWithChain/TRBPercents",
-            valueType: "Double",
-            annotations: {
-                "pl7.app/min": "0",
-                "pl7.app/max": "100",
-                "pl7.app/table/orderPriority": "97100",
-                "pl7.app/table/visibility": "default",
-                "pl7.app/label": "Reads with Chain TRB (%)"
-            }
-        }
-    },
-    {
-        column: "align.readsWithChain.TRG",
-        id: "align-reads-with-chain-trg",
-        allowNA: true,
-        naRegex: "",
-        spec: {
-            name: "mixcr.com/reports/align/readsWithChain/TRG",
-            valueType: "Long",
-            annotations: {
-                "pl7.app/min": "0",
-                "pl7.app/table/orderPriority": "97200",
-                "pl7.app/table/visibility": "optional",
-                "pl7.app/label": "Reads with Chain TRG"
-            }
-        }
-    },
-    {
-        column: "align.readsWithChain.TRGPercents",
-        id: "align-reads-with-chain-trg-percents",
-        allowNA: true,
-        naRegex: "",
-        spec: {
-            name: "mixcr.com/reports/align/readsWithChain/TRGPercents",
-            valueType: "Double",
-            annotations: {
-                "pl7.app/min": "0",
-                "pl7.app/max": "100",
-                "pl7.app/table/orderPriority": "97300",
-                "pl7.app/table/visibility": "default",
-                "pl7.app/label": "Reads with Chain TRG (%)"
-            }
-        }
-    },
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
     {
         column: "assembleCells.cellBarcodesWithFoundGroups",
         id: "assemble-cells-cell-barcodes-with-found-groups",
@@ -1180,93 +1180,96 @@ 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"
-            }
-        }
-    },
-    {
-        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.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.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 (%)"
-            }
-        }
     }]
 
-    for chain in chains {
+    for cellTag in cellTags {
         singleCellColumns += [{
-            column: "clonesWithChain." + chain,
-            id: "clones-with-chain-" + chain,
+            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." + 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." + cellTag + ".outputDiversity",
+            id: "refine-tags-" + cellTag + "-output-diversity",
             allowNA: true,
-            naRegex: "",
+            naRegex: "NaN",
             spec: {
-                name: "mixcr.com/reports/clonesWithChain/" + chain,
+                name: "mixcr.com/reports/refineTags/CELL/outputDiversity",
                 valueType: "Long",
                 annotations: {
                     "pl7.app/min": "0",
-                    "pl7.app/table/orderPriority": "97400",
+                    "pl7.app/table/orderPriority": "86000",
                     "pl7.app/table/visibility": "optional",
-                    "pl7.app/label": "Clones with Chain " + chain
+                    "pl7.app/label": "Refine Tags " + cellTag + " - 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 (%)"
                 }
             }
         }]
     }
 
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
     columns := baseColumns
     if hasUmi {
         columns = columns + dataWithUmiColumns