From 7ef00a2c780051e810af78a2f91b574e50800741 Mon Sep 17 00:00:00 2001
From: Dmitry Bolotin <bolotin.dmitriy@gmail.com>
Date: Sat, 7 Sep 2024 19:42:29 +0200
Subject: [PATCH] fixes and improvements

---
 test/src/wf.test.ts                           |    8 +
 .../src/calculate-pfconv-params.tpl.tengo     |   17 +-
 workflow/src/main.tpl.tengo                   |   12 +-
 workflow/src/pfconv_params.lib.tengo          | 1403 ++++++++---------
 workflow/src/process.tpl.tengo                |   22 +
 5 files changed, 749 insertions(+), 713 deletions(-)

diff --git a/test/src/wf.test.ts b/test/src/wf.test.ts
index 08d88de..86d9328 100644
--- a/test/src/wf.test.ts
+++ b/test/src/wf.test.ts
@@ -165,6 +165,14 @@ blockTest(
 
     const clonesPfColumnList = await ml.driverKit.pFrameDriver.listColumns(clonesPfHandle);
 
+    expect(
+      clonesPfColumnList[0].spec.axesSpec.find((s: any) => s.name === 'pl7.app/vdj/cloneId')
+    ).toMatchObject({
+      domain: {
+        'pl7.app/blockId': clonotypingBlockId
+      }
+    });
+
     // console.log(clonesPfColumnList);
     expect(clonesPfColumnList).length.to.greaterThanOrEqual(7);
 
diff --git a/workflow/src/calculate-pfconv-params.tpl.tengo b/workflow/src/calculate-pfconv-params.tpl.tengo
index 5cbc08f..810739f 100644
--- a/workflow/src/calculate-pfconv-params.tpl.tengo
+++ b/workflow/src/calculate-pfconv-params.tpl.tengo
@@ -1,14 +1,26 @@
 // calculate-pfconv-params
 self := import("@milaboratory/tengo-sdk:tpl")
+// validation := import("@milaboratory/tengo-sdk:validation")
 
-pvconfParams := import(":pfconv_params")
+pvconfParamsLib := import(":pfconv_params")
 
 json := import("json")
 
+// self.validateInputs({
+// 	"__options__,closed": "",
+// 	"request": {
+// 		"__options__,closed": "",
+// 		"blockId": ["not", validation.resource()],
+// 		"specs,omitempty": ["not", validation.resource()]
+// 	}
+// })
+
 self.defineOutputs("params")
 
 self.body(func(inputs) {
 
+	blockId := inputs.blockId
+
 	// filter function
 	filter := func(list, predicate) {
 		result := []
@@ -33,6 +45,7 @@ self.body(func(inputs) {
 	// get specs and preset data
 	specs := inputs.specs.getDataAsJson()
 	preset := inputs.preset.getDataAsJson()
+
 	//if using readCount or umiCount
 	columnsList := []
 	columnsOrder := []
@@ -63,6 +76,8 @@ self.body(func(inputs) {
 		}
 	}
 
+	pvconfParams := pvconfParamsLib.getColumns(blockId)
+
 	// filter pvconfParams by column name and get a list of fields from it
 	columns := []
 	for col in columnsList {
diff --git a/workflow/src/main.tpl.tengo b/workflow/src/main.tpl.tengo
index 6a80b67..d0deb28 100644
--- a/workflow/src/main.tpl.tengo
+++ b/workflow/src/main.tpl.tengo
@@ -20,6 +20,8 @@ processTpl := assets.importTemplate(":process")
 wf.setPreRun(assets.importTemplate(":prerun"))
 
 wf.body(func(args) {
+	blockId := wf.blockId().getDataAsJson()
+
 	inputRef := args.input
 
 	preset := args.preset
@@ -38,6 +40,7 @@ wf.body(func(args) {
 	specsContent := getPreset.output("presetSpecForBack", 24 * 60 * 60 * 1000)
 
 	calculatePfconvParams := render.create(calculatePfconvParamsTpl, {
+		blockId: blockId,
 		preset: presetContent,
 		specs: specsContent
 	})
@@ -46,7 +49,8 @@ wf.body(func(args) {
 	runMixcr := render.createEphemeral(processTpl, {
 		params: smart.createJsonResource({
 			preset: preset,
-			species: species
+			species: species,
+			blockId: blockId
 		}),
 		presetContent: specsContent,
 		pfconvParams: pfconvParams,
@@ -63,7 +67,11 @@ wf.body(func(args) {
 			spec: runMixcr.output("reports.spec"),
 			data: runMixcr.output("reports.data")
 		},
-		clones: runMixcr.output("clones")
+		clones: runMixcr.output("clones"),
+		clns: {
+			spec: runMixcr.output("clns.spec"),
+			data: runMixcr.output("clns.data")
+		}
 	}
 
 	outputs := {
diff --git a/workflow/src/pfconv_params.lib.tengo b/workflow/src/pfconv_params.lib.tengo
index b740d57..2e7ce8d 100644
--- a/workflow/src/pfconv_params.lib.tengo
+++ b/workflow/src/pfconv_params.lib.tengo
@@ -1,712 +1,695 @@
-export {
-	"axes": [
-		{
-			"column": "cloneId",
-			"spec": {
-				"name": "pl7.app/vdj/cloneId",
-				"type": "Long",
-				"annotations": {
-					"pl7.app/label": "Clone id"
-				}
-			}
-		}, {
-			"column": "tagValueCELL",
-			"spec": {
-				"name": "pl7.app/vdj/tagValueCELL",
-				"type": "String",
-				"annotations": {
-					"pl7.app/label": "Cell tag"
-				}
-			}
-		}
-		],
-	"columns": [
-		{
-			"column": "cellGroup",
-			"id": "cell-group",
-			"allowNA": false,
-			"spec": {
-				"name": "pl7.app/vdj/cellGroup",
-				"valueType": "Long",
-				"annotations": {
-					"pl7.app/label": "Cell group number"
-				}
-			}
-		}, {
-			"column": "readCount",
-			"id": "read-count",
-			"allowNA": false,
-			"spec": {
-				"name": "pl7.app/vdj/readCount",
-				"valueType": "Long",
-				"annotations": {
-					"pl7.app/label": "Number Of Reads"
-				}
-			}
-		}, {
-			"column": "readFraction",
-			"id": "read-fraction",
-			"allowNA": false,
-			"spec": {
-				"name": "pl7.app/vdj/readFraction",
-				"valueType": "Float",
-				"annotations": {
-					"pl7.app/label": "Fraction of reads"
-				}
-			}
-		}, {
-			"column": "uniqueMoleculeCount",
-			"id": "umi-count",
-			"allowNA": false,
-			"spec": {
-				"name": "pl7.app/vdj/uniqueMoleculeCount",
-				"valueType": "Long",
-				"annotations": {
-					"pl7.app/label": "Number of UMI"
-				}
-			}
-		}, {
-			"column": "uniqueMoleculeFraction",
-			"id": "umi-fraction",
-			"allowNA": false,
-			"spec": {
-				"name": "pl7.app/vdj/uniqueMoleculeFraction",
-				"valueType": "Float",
-				"annotations": {
-					"pl7.app/label": "Fraction of UMI"
-				}
-			}
-		}, {
-			"column": "targetSequences",
-			"id": "n-seq-clonal-sequences",
-			"allowNA": false,
-			"spec": {
-				"name": "pl7.app/vdj/sequence",
-				"valueType": "String",
-				"domain": {
-					"pl7.app/vdj/sequence": "clonalSequence",
-					"pl7.app/alphabet": "nucleotide"
-				},
-				"annotations": {
-					"pl7.app/type": "sequence",
-					"pl7.app/label": "Clonal sequences"
-				}
-			}
-		}, {
-			"column": "targetQualities",
-			"id": "clonal-qualities",
-			"allowNA": false,
-			"spec": {
-				"name": "pl7.app/vdj/sequenceQuality",
-				"valueType": "String",
-				"domain": {
-					"pl7.app/vdj/quality": "clonalQuality"
-				},
-				"annotations": {
-					"type": "quality string",
-					"pl7.app/label": "Clonal qualities"
-				}
-			}
-		}, {
-			"column": "bestVHit",
-			"id": "best-v-hit",
-			"allowNA": false,
-			"spec": {
-				"name": "pl7.app/vdj/geneHit",
-				"valueType": "String",
-				"domain": {
-					"pl7.app/vdj/reference": "VGene"
-				},
-				"annotations": {
-					"type": "V gene name",
-					"pl7.app/label": "Best V hit"
-				}
-			}
-		}, {
-			"column": "bestDHit",
-			"id": "best-d-hit",
-			"spec": {
-				"name": "pl7.app/vdj/geneHit",
-				"valueType": "String",
-				"domain": {
-					"pl7.app/vdj/reference": "DGene"
-				},
-				"annotations": {
-					"type": "D gene name",
-					"pl7.app/label": "Best D hit"
-				}
-			}
-		}, {
-			"column": "bestJHit",
-			"id": "best-j-hit",
-			"allowNA": false,
-			"spec": {
-				"name": "pl7.app/vdj/geneHit",
-				"valueType": "String",
-				"domain": {
-					"pl7.app/vdj/reference": "JGene"
-				},
-				"annotations": {
-					"type": "J gene name",
-					"pl7.app/label": "Best J hit"
-				}
-			}
-		}, {
-			"column": "bestCHit",
-			"id": "best-c-hit",
-			"spec": {
-				"name": "pl7.app/vdj/geneHit",
-				"valueType": "String",
-				"domain": {
-					"pl7.app/vdj/reference": "CGene"
-				},
-				"annotations": {
-					"type": "C gene name",
-					"pl7.app/label": "Best C hit"
-				}
-			}
-		}, {
-			"column": "nSeqFR1",
-			"id": "n-seq-fr1",
-			"spec": {
-				"name": "pl7.app/vdj/sequence",
-				"valueType": "String",
-				"domain": {
-					"pl7.app/vdj/feature": "FR1",
-					"pl7.app/alphabet": "nucleotide"
-				},
-				"annotations": {
-					"type": "sequence",
-					"pl7.app/label": "FR1 nt"
-				}
-			}
-		}, {
-			"column": "minQualFR1",
-			"id": "min-qual-fr1",
-			"spec": {
-				"name": "pl7.app/vdj/sequenceQuality",
-				"valueType": "Int",
-				"domain": {
-					"pl7.app/vdj/quality": "minQuality",
-					"pl7.app/vdj/feature": "FR1"
-				},
-				"annotations": {
-					"pl7.app/label": "Min quality FR1"
-				}
-			}
-		}, {
-			"column": "nSeqFR2",
-			"id": "n-seq-fr2",
-			"spec": {
-				"name": "pl7.app/vdj/sequence",
-				"valueType": "String",
+ll := import("@milaboratory/tengo-sdk:ll")
 
-				"domain": {
-					"pl7.app/vdj/feature": "FR2",
-					"pl7.app/alphabet": "nucleotide"
-				},
-				"annotations": {
-					"type": "sequence",
-					"pl7.app/label": "FR2 nt"
-				}
-			}
-		}, {
-			"column": "minQualFR2",
-			"id": "min-qual-fr2",
-			"spec": {
-				"name": "pl7.app/vdj/sequenceQuality",
-				"valueType": "Int",
-				"domain": {
-					"pl7.app/vdj/quality": "minQuality",
-					"pl7.app/vdj/feature": "FR2"
-				},
-				"annotations": {
-					"pl7.app/label": "Min quality FR2"
-				}
-			}
-		}, {
-			"column": "nSeqFR3",
-			"id": "n-seq-fr3",
-			"spec": {
-				"name": "pl7.app/vdj/sequence",
-				"valueType": "String",
-				"domain": {
-					"pl7.app/vdj/feature": "FR3",
-					"pl7.app/alphabet": "nucleotide"
-				},
-				"annotations": {
-					"type": "sequence",
-					"pl7.app/label": "FR3 nt"
-				}
-			}
-		}, {
-			"column": "minQualFR3",
-			"id": "min-qual-fr3",
-			"spec": {
-				"name": "pl7.app/vdj/sequenceQuality",
-				"valueType": "Int",
-				"domain": {
-					"pl7.app/vdj/quality": "minQuality",
-					"pl7.app/vdj/feature": "FR3"
-				},
-				"annotations": {
-					"pl7.app/label": "Min quality FR3"
-				}
-			}
-		}, {
-			"column": "nSeqFR4",
-			"id": "n-seq-fr4",
-			"spec": {
-				"name": "pl7.app/vdj/sequence",
-				"valueType": "String",
-				"domain": {
-					"pl7.app/vdj/feature": "FR4",
-					"pl7.app/alphabet": "nucleotide"
-				},
-				"annotations": {
-					"type": "sequence",
-					"pl7.app/label": "FR4 nt"
-				}
-			}
-		}, {
-			"column": "minQualFR4",
-			"id": "min-qual-fr4",
-			"spec": {
-				"name": "pl7.app/vdj/sequenceQuality",
-				"valueType": "Int",
-				"domain": {
-					"pl7.app/vdj/quality": "minQuality",
-					"pl7.app/vdj/feature": "FR4"
-				},
-				"annotations": {
-					"pl7.app/label": "Min quality FR4"
-				}
-			}
-		}, {
-			"column": "nSeqCDR1",
-			"id": "n-seq-cdr1",
-			"spec": {
-				"name": "pl7.app/vdj/sequence",
-				"valueType": "String",
-				"domain": {
-					"pl7.app/vdj/feature": "CDR1",
-					"pl7.app/alphabet": "nucleotide"
-				},
-				"annotations": {
-					"type": "sequence",
-					"pl7.app/label": "CDR1 nt"
-				}
-			}
-		}, {
-			"column": "minQualCDR1",
-			"id": "min-qual-cdr1",
-			"spec": {
-				"name": "pl7.app/vdj/minQualCDR1",
-				"valueType": "Int",
-				"domain": {
-					"pl7.app/vdj/quality": "minQuality",
-					"pl7.app/vdj/feature": "CDR1"
-				},
-				"annotations": {
-					"pl7.app/label": "Min quality CDR1"
-				}
-			}
-		}, {
-			"column": "nSeqCDR2",
-			"id": "n-seq-cdr2",
-			"spec": {
-				"name": "pl7.app/vdj/sequence",
-				"valueType": "String",
-				"domain": {
-					"pl7.app/vdj/feature": "CDR2",
-					"pl7.app/alphabet": "nucleotide"
-				},
-				"annotations": {
-					"type": "sequence",
-					"pl7.app/label": "CDR2 nt"
-				}
-			}
-		}, {
-			"column": "minQualCDR2",
-			"id": "min-qual-cdr2",
-			"spec": {
-				"name": "pl7.app/vdj/sequenceQuality",
-				"valueType": "Int",
-				"domain": {
-					"pl7.app/vdj/quality": "minQuality",
-					"pl7.app/vdj/feature": "CDR2"
-				},
-				"annotations": {
-					"pl7.app/label": "Min quality CDR2"
-				}
-			}
-		}, {
-			"column": "nSeqCDR3",
-			"id": "n-seq-cdr3",
-			"spec": {
-				"valueType": "String",
-				"name": "pl7.app/vdj/sequence",
-				"domain": {
-					"pl7.app/vdj/feature": "CDR3",
-					"pl7.app/alphabet": "nucleotide"
-				},
-				"annotations": {
-					"type": "sequence",
-					"pl7.app/label": "CDR3 nt"
-				}
-			}
-		}, {
-			"column": "minQualCDR3",
-			"id": "min-qual-cdr3",
-			"spec": {
-				"name": "pl7.app/vdj/sequenceQuality",
-				"valueType": "Int",
-				"domain": {
-					"pl7.app/vdj/quality": "minQuality",
-					"pl7.app/vdj/feature": "CDR3"
-				},
-				"annotations": {
-					"pl7.app/label": "Min quality CDR3"
-				}
-			}
-		}, {
-			"column": "aaSeqFR1",
-			"id": "aa-seq-fr1",
-			"spec": {
-				"valueType": "String",
-				"name": "pl7.app/vdj/sequence",
-				"domain": {
-					"pl7.app/vdj/feature": "FR1",
-					"alphabet": "aminoacid"
-				},
-				"annotations": {
-					"type": "sequence",
-					"pl7.app/label": "FR1 aa"
-				}
-			}
-		}, {
-			"column": "aaSeqFR2",
-			"id": "aa-seq-fr2",
-			"spec": {
-				"valueType": "String",
-				"name": "pl7.app/vdj/sequence",
-				"domain": {
-					"pl7.app/vdj/feature": "FR2",
-					"alphabet": "aminoacid"
-				},
-				"annotations": {
-					"type": "sequence",
-					"pl7.app/label": "FR2 aa"
-				}
-			}
-		}, {
-			"column": "aaSeqFR3",
-			"id": "aa-seq-fr3",
-			"spec": {
-				"valueType": "String",
-				"name": "pl7.app/vdj/sequence",
-				"domain": {
-					"pl7.app/vdj/feature": "FR3",
-					"alphabet": "aminoacid"
-				},
-				"annotations": {
-					"type": "sequence",
-					"pl7.app/label": "FR3 aa"
-				}
-			}
-		}, {
-			"column": "aaSeqFR4",
-			"id": "aa-seq-fr4",
-			"spec": {
-				"valueType": "String",
-				"name": "pl7.app/vdj/sequence",
-				"domain": {
-					"pl7.app/vdj/feature": "FR4",
-					"alphabet": "aminoacid"
-				},
-				"annotations": {
-					"type": "sequence",
-					"pl7.app/label": "FR4 aa"
-				}
-			}
-		}, {
-			"column": "aaSeqCDR1",
-			"id": "aa-seq-cdr1",
-			"spec": {
-				"valueType": "String",
-				"name": "pl7.app/vdj/sequence",
-				"domain": {
-					"pl7.app/vdj/feature": "CDR1",
-					"alphabet": "aminoacid"
-				},
-				"annotations": {
-					"type": "sequence",
-					"pl7.app/label": "CDR1 aa"
-				}
-			}
-		}, {
-			"column": "aaSeqCDR2",
-			"id": "aa-seq-cdr2",
-			"spec": {
-				"valueType": "String",
-				"name": "pl7.app/vdj/sequence",
-				"domain": {
-					"pl7.app/vdj/feature": "CDR2",
-					"alphabet": "aminoacid"
-				},
-				"annotations": {
-					"type": "sequence",
-					"pl7.app/label": "CDR2 aa"
-				}
-			}
-		}, {
-			"column": "aaSeqCDR3",
-			"id": "aa-seq-cdr3",
-			"spec": {
-				"valueType": "String",
-				"name": "pl7.app/vdj/sequence",
-				"domain": {
-					"pl7.app/vdj/feature": "CDR3",
-					"alphabet": "aminoacid"
-				},
-				"annotations": {
-					"type": "sequence",
-					"pl7.app/label": "CDR3 aa"
-				}
-			}
-		}, {
-			"column": "nSeqImputedFR1",
-			"id": "n-seq-imputed-fr1",
-			"spec": {
-				"name": "pl7.app/vdj/sequence",
-				"valueType": "String",
-				"domain": {
-					"pl7.app/vdj/feature": "FR1",
-					"alphabet": "nucleotide"
-				},
-				"annotations": {
-					"type": "sequence",
-					"pl7.app/label": "FR1 imputed nt"
-				}
-			}
-		}, {
-			"column": "nSeqImputedFR2",
-			"id": "n-seq-imputed-fr2",
-			"spec": {
-				"name": "pl7.app/vdj/sequence",
-				"valueType": "String",
-				"domain": {
-					"pl7.app/vdj/feature": "FR2",
-					"alphabet": "nucleotide"
-				},
-				"annotations": {
-					"type": "sequence",
-					"pl7.app/label": "FR2 imputed nt"
-				}
-			}
-		}, {
-			"column": "nSeqImputedFR3",
-			"id": "n-seq-imputed-fr3",
-			"spec": {
-				"name": "pl7.app/vdj/sequence",
-				"valueType": "String",
-				"domain": {
-					"pl7.app/vdj/feature": "FR3",
-					"alphabet": "nucleotide"
-				},
-				"annotations": {
-					"type": "sequence",
-					"pl7.app/label": "FR3 imputed nt"
-				}
-			}
-		}, {
-			"column": "nSeqImputedFR4",
-			"id": "n-seq-imputed-fr4",
-			"spec": {
-				"name": "pl7.app/vdj/sequence",
-				"valueType": "String",
-				"domain": {
-					"pl7.app/vdj/feature": "FR4",
-					"alphabet": "nucleotide"
-				},
-				"annotations": {
-					"type": "sequence",
-					"pl7.app/label": "FR4 imputed nt"
-				}
-			}
-		}, {
-			"column": "nSeqImputedCDR1",
-			"id": "n-seq-imputed-cdr1",
-			"spec": {
-				"name": "pl7.app/vdj/sequence",
-				"valueType": "String",
-				"domain": {
-					"pl7.app/vdj/feature": "CDR1",
-					"alphabet": "nucleotide"
-				},
-				"annotations": {
-					"type": "sequence",
-					"pl7.app/label": "CDR1 imputed nt"
-				}
-			}
-		}, {
-			"column": "nSeqImputedCDR2",
-			"id": "n-seq-imputed-cdr2",
-			"spec": {
-				"name": "pl7.app/vdj/sequence",
-				"valueType": "String",
-				"domain": {
-					"pl7.app/vdj/feature": "CDR2",
-					"alphabet": "nucleotide"
-				},
-				"annotations": {
-					"type": "sequence",
-					"pl7.app/label": "CDR2 imputed nt"
-				}
-			}
-		}, {
-			"column": "nSeqImputedCDR3",
-			"id": "n-seq-imputed-CDR3",
-			"spec": {
-				"name": "pl7.app/vdj/sequence",
-				"valueType": "String",
-				"domain": {
-					"pl7.app/vdj/feature": "CDR3",
-					"alphabet": "nucleotide"
-				},
-				"annotations": {
-					"type": "sequence",
-					"pl7.app/label": "CDR3 imputed nt"
-				}
-			}
-		}, {
-			"column": "aaSeqImputedFR1",
-			"id": "aa-seq-imputed-fr1",
-			"spec": {
-				"valueType": "String",
-				"name": "pl7.app/vdj/sequence",
-				"domain": {
-					"pl7.app/vdj/feature": "FR1",
-					"alphabet": "aminoacid"
-				},
-				"annotations": {
-					"type": "sequence",
-					"pl7.app/label": "FR1 imputed aa"
-				}
-			}
-		}, {
-			"column": "aaSeqImputedFR2",
-			"id": "aa-seq-imputed-fr2",
-			"spec": {
-				"valueType": "String",
-				"name": "pl7.app/vdj/sequence",
-				"domain": {
-					"pl7.app/vdj/feature": "FR2",
-					"alphabet": "aminoacid"
-				},
-				"annotations": {
-					"type": "sequence",
-					"pl7.app/label": "FR2 imputed aa"
-				}
-			}
-		}, {
-			"column": "aaSeqImputedFR3",
-			"id": "aa-seq-imputed-fr3",
-			"spec": {
-				"valueType": "String",
-				"name": "pl7.app/vdj/sequence",
-				"domain": {
-					"pl7.app/vdj/feature": "FR3",
-					"alphabet": "aminoacid"
-				},
-				"annotations": {
-					"type": "sequence",
-					"pl7.app/label": "FR3 imputed aa"
-				}
-			}
-		}, {
-			"column": "aaSeqImputedFR4",
-			"id": "aa-seq-imputed-fr4",
-			"spec": {
-				"valueType": "String",
-				"name": "pl7.app/vdj/sequence",
-				"domain": {
-					"pl7.app/vdj/feature": "FR4",
-					"alphabet": "aminoacid"
-				},
-				"annotations": {
-					"type": "sequence",
-					"pl7.app/label": "FR4 imputed aa"
-				}
-			}
-		}, {
-			"column": "aaSeqImputedCDR1",
-			"id": "aa-seq-imputed-cdr1",
-			"spec": {
-				"valueType": "String",
-				"name": "pl7.app/vdj/sequence",
-				"domain": {
-					"pl7.app/vdj/feature": "CDR1",
-					"alphabet": "aminoacid"
-				},
-				"annotations": {
-					"type": "sequence",
-					"pl7.app/label": "CDR1 imputed aa"
-				}
-			}
-		}, {
-			"column": "aaSeqImputedCDR2",
-			"id": "aa-seq-imputed-cdr2",
-			"spec": {
-				"valueType": "String",
-				"name": "pl7.app/vdj/sequence",
-				"domain": {
-					"pl7.app/vdj/feature": "CDR2",
-					"alphabet": "aminoacid"
-				},
-				"annotations": {
-					"type": "sequence",
-					"pl7.app/label": "CDR2 imputed aa"
-				}
-			}
-		}, {
-			"column": "aaSeqImputedCDR3",
-			"id": "aa-seq-imputed-CDR3",
-			"spec": {
-				"valueType": "String",
-				"name": "pl7.app/vdj/sequence",
-				"domain": {
-					"pl7.app/vdj/feature": "CDR3",
-					"alphabet": "aminoacid"
-				},
-				"annotations": {
-					"type": "sequence",
-					"pl7.app/label": "CDR3 imputed aa"
-				}
-			}
-		}, {
-			"column": "isotype",
-			"id": "isotype",
-			"spec": {
-				"valueType": "String",
-				"name": "pl7.app/vdj/isotype",
-				"annotations": {
-					"pl7.app/label": "IG isotype"
-				}
-			}
-		}, {
-			"column": "topChains",
-			"id": "top-chains",
-			"allowNA": false,
-			"spec": {
-				"valueType": "String",
-				"name": "pl7.app/vdj/chain",
-				"annotations": {
-					"pl7.app/label": "Chain"
-				}
-			}
-		}
-		],
-	"storageFormat": "Binary",
-	"partitionKeyLength": 0
+getColumns := func(blockId) {
+  return {
+    "axes": [
+      {
+        "column": "cloneId",
+        "spec": {
+          "name": "pl7.app/vdj/cloneId",
+          "type": "Long",
+          "domain": {
+            "pl7.app/blockId": blockId
+          },
+          "annotations": {
+            "pl7.app/label": "Clone id"
+          }
+        }
+      }, {
+        "column": "tagValueCELL",
+        "spec": {
+          "name": "pl7.app/vdj/tagValueCELL",
+          "type": "String",
+          "annotations": {
+            "pl7.app/label": "Cell tag"
+          }
+        }
+      }
+      ],
+    "columns": [
+      {
+        "column": "cellGroup",
+        "id": "cell-group",
+        "allowNA": false,
+        "spec": {
+          "name": "pl7.app/vdj/cellGroup",
+          "valueType": "Long",
+          "annotations": {
+            "pl7.app/label": "Cell group number"
+          }
+        }
+      }, {
+        "column": "readCount",
+        "id": "read-count",
+        "allowNA": false,
+        "spec": {
+          "name": "pl7.app/vdj/readCount",
+          "valueType": "Long",
+          "annotations": {
+            "pl7.app/label": "Number Of Reads"
+          }
+        }
+      }, {
+        "column": "readFraction",
+        "id": "read-fraction",
+        "allowNA": false,
+        "spec": {
+          "name": "pl7.app/vdj/readFraction",
+          "valueType": "Double",
+          "annotations": {
+            "pl7.app/label": "Fraction of reads"
+          }
+        }
+      }, {
+        "column": "uniqueMoleculeCount",
+        "id": "umi-count",
+        "allowNA": false,
+        "spec": {
+          "name": "pl7.app/vdj/uniqueMoleculeCount",
+          "valueType": "Long",
+          "annotations": {
+            "pl7.app/label": "Number of UMI"
+          }
+        }
+      }, {
+        "column": "uniqueMoleculeFraction",
+        "id": "umi-fraction",
+        "allowNA": false,
+        "spec": {
+          "name": "pl7.app/vdj/uniqueMoleculeFraction",
+          "valueType": "Double",
+          "annotations": {
+            "pl7.app/label": "Fraction of UMI"
+          }
+        }
+      }, {
+        "column": "targetSequences",
+        "id": "n-seq-clonal-sequences",
+        "allowNA": false,
+        "spec": {
+          "name": "pl7.app/vdj/sequence",
+          "valueType": "String",
+          "domain": {
+            "pl7.app/vdj/sequence": "clonalSequence",
+            "pl7.app/alphabet": "nucleotide"
+          },
+          "annotations": {
+            "pl7.app/type": "sequence",
+            "pl7.app/label": "Clonal sequences"
+          }
+        }
+      }, {
+        "column": "targetQualities",
+        "id": "clonal-qualities",
+        "allowNA": false,
+        "spec": {
+          "name": "pl7.app/vdj/sequenceQuality",
+          "valueType": "String",
+          "domain": {
+            "pl7.app/vdj/quality": "clonalQuality"
+          },
+          "annotations": {
+            "type": "quality string",
+            "pl7.app/label": "Clonal qualities"
+          }
+        }
+      }, {
+        "column": "bestVHit",
+        "id": "best-v-hit",
+        "allowNA": false,
+        "spec": {
+          "name": "pl7.app/vdj/geneHit",
+          "valueType": "String",
+          "domain": {
+            "pl7.app/vdj/reference": "VGene"
+          },
+          "annotations": {
+            "type": "V gene name",
+            "pl7.app/label": "Best V hit"
+          }
+        }
+      }, {
+        "column": "bestDHit",
+        "id": "best-d-hit",
+        "spec": {
+          "name": "pl7.app/vdj/geneHit",
+          "valueType": "String",
+          "domain": {
+            "pl7.app/vdj/reference": "DGene"
+          },
+          "annotations": {
+            "type": "D gene name",
+            "pl7.app/label": "Best D hit"
+          }
+        }
+      }, {
+        "column": "bestJHit",
+        "id": "best-j-hit",
+        "allowNA": false,
+        "spec": {
+          "name": "pl7.app/vdj/geneHit",
+          "valueType": "String",
+          "domain": {
+            "pl7.app/vdj/reference": "JGene"
+          },
+          "annotations": {
+            "type": "J gene name",
+            "pl7.app/label": "Best J hit"
+          }
+        }
+      }, {
+        "column": "bestCHit",
+        "id": "best-c-hit",
+        "spec": {
+          "name": "pl7.app/vdj/geneHit",
+          "valueType": "String",
+          "domain": {
+            "pl7.app/vdj/reference": "CGene"
+          },
+          "annotations": {
+            "type": "C gene name",
+            "pl7.app/label": "Best C hit"
+          }
+        }
+      }, {
+        "column": "nSeqFR1",
+        "id": "n-seq-fr1",
+        "spec": {
+          "name": "pl7.app/vdj/sequence",
+          "valueType": "String",
+          "domain": {
+            "pl7.app/vdj/feature": "FR1",
+            "pl7.app/alphabet": "nucleotide"
+          },
+          "annotations": {
+            "pl7.app/label": "FR1 nt"
+          }
+        }
+      }, {
+        "column": "minQualFR1",
+        "id": "min-qual-fr1",
+        "spec": {
+          "name": "pl7.app/vdj/sequenceQuality",
+          "valueType": "Int",
+          "domain": {
+            "pl7.app/vdj/quality": "minQuality",
+            "pl7.app/vdj/feature": "FR1"
+          },
+          "annotations": {
+            "pl7.app/label": "Min quality FR1"
+          }
+        }
+      }, {
+        "column": "nSeqFR2",
+        "id": "n-seq-fr2",
+        "spec": {
+          "name": "pl7.app/vdj/sequence",
+          "valueType": "String",
+
+          "domain": {
+            "pl7.app/vdj/feature": "FR2",
+            "pl7.app/alphabet": "nucleotide"
+          },
+          "annotations": {
+            "pl7.app/label": "FR2 nt"
+          }
+        }
+      }, {
+        "column": "minQualFR2",
+        "id": "min-qual-fr2",
+        "spec": {
+          "name": "pl7.app/vdj/sequenceQuality",
+          "valueType": "Int",
+          "domain": {
+            "pl7.app/vdj/quality": "minQuality",
+            "pl7.app/vdj/feature": "FR2"
+          },
+          "annotations": {
+            "pl7.app/label": "Min quality FR2"
+          }
+        }
+      }, {
+        "column": "nSeqFR3",
+        "id": "n-seq-fr3",
+        "spec": {
+          "name": "pl7.app/vdj/sequence",
+          "valueType": "String",
+          "domain": {
+            "pl7.app/vdj/feature": "FR3",
+            "pl7.app/alphabet": "nucleotide"
+          },
+          "annotations": {
+            "pl7.app/label": "FR3 nt"
+          }
+        }
+      }, {
+        "column": "minQualFR3",
+        "id": "min-qual-fr3",
+        "spec": {
+          "name": "pl7.app/vdj/sequenceQuality",
+          "valueType": "Int",
+          "domain": {
+            "pl7.app/vdj/quality": "minQuality",
+            "pl7.app/vdj/feature": "FR3"
+          },
+          "annotations": {
+            "pl7.app/label": "Min quality FR3"
+          }
+        }
+      }, {
+        "column": "nSeqFR4",
+        "id": "n-seq-fr4",
+        "spec": {
+          "name": "pl7.app/vdj/sequence",
+          "valueType": "String",
+          "domain": {
+            "pl7.app/vdj/feature": "FR4",
+            "pl7.app/alphabet": "nucleotide"
+          },
+          "annotations": {
+            "pl7.app/label": "FR4 nt"
+          }
+        }
+      }, {
+        "column": "minQualFR4",
+        "id": "min-qual-fr4",
+        "spec": {
+          "name": "pl7.app/vdj/sequenceQuality",
+          "valueType": "Int",
+          "domain": {
+            "pl7.app/vdj/quality": "minQuality",
+            "pl7.app/vdj/feature": "FR4"
+          },
+          "annotations": {
+            "pl7.app/label": "Min quality FR4"
+          }
+        }
+      }, {
+        "column": "nSeqCDR1",
+        "id": "n-seq-cdr1",
+        "spec": {
+          "name": "pl7.app/vdj/sequence",
+          "valueType": "String",
+          "domain": {
+            "pl7.app/vdj/feature": "CDR1",
+            "pl7.app/alphabet": "nucleotide"
+          },
+          "annotations": {
+            "pl7.app/label": "CDR1 nt"
+          }
+        }
+      }, {
+        "column": "minQualCDR1",
+        "id": "min-qual-cdr1",
+        "spec": {
+          "name": "pl7.app/vdj/minQualCDR1",
+          "valueType": "Int",
+          "domain": {
+            "pl7.app/vdj/quality": "minQuality",
+            "pl7.app/vdj/feature": "CDR1"
+          },
+          "annotations": {
+            "pl7.app/label": "Min quality CDR1"
+          }
+        }
+      }, {
+        "column": "nSeqCDR2",
+        "id": "n-seq-cdr2",
+        "spec": {
+          "name": "pl7.app/vdj/sequence",
+          "valueType": "String",
+          "domain": {
+            "pl7.app/vdj/feature": "CDR2",
+            "pl7.app/alphabet": "nucleotide"
+          },
+          "annotations": {
+            "pl7.app/label": "CDR2 nt"
+          }
+        }
+      }, {
+        "column": "minQualCDR2",
+        "id": "min-qual-cdr2",
+        "spec": {
+          "name": "pl7.app/vdj/sequenceQuality",
+          "valueType": "Int",
+          "domain": {
+            "pl7.app/vdj/quality": "minQuality",
+            "pl7.app/vdj/feature": "CDR2"
+          },
+          "annotations": {
+            "pl7.app/label": "Min quality CDR2"
+          }
+        }
+      }, {
+        "column": "nSeqCDR3",
+        "id": "n-seq-cdr3",
+        "spec": {
+          "valueType": "String",
+          "name": "pl7.app/vdj/sequence",
+          "domain": {
+            "pl7.app/vdj/feature": "CDR3",
+            "pl7.app/alphabet": "nucleotide"
+          },
+          "annotations": {
+            "pl7.app/label": "CDR3 nt"
+          }
+        }
+      }, {
+        "column": "minQualCDR3",
+        "id": "min-qual-cdr3",
+        "spec": {
+          "name": "pl7.app/vdj/sequenceQuality",
+          "valueType": "Int",
+          "domain": {
+            "pl7.app/vdj/quality": "minQuality",
+            "pl7.app/vdj/feature": "CDR3"
+          },
+          "annotations": {
+            "pl7.app/label": "Min quality CDR3"
+          }
+        }
+      }, {
+        "column": "aaSeqFR1",
+        "id": "aa-seq-fr1",
+        "spec": {
+          "valueType": "String",
+          "name": "pl7.app/vdj/sequence",
+          "domain": {
+            "pl7.app/vdj/feature": "FR1",
+            "alphabet": "aminoacid"
+          },
+          "annotations": {
+            "pl7.app/label": "FR1 aa"
+          }
+        }
+      }, {
+        "column": "aaSeqFR2",
+        "id": "aa-seq-fr2",
+        "spec": {
+          "valueType": "String",
+          "name": "pl7.app/vdj/sequence",
+          "domain": {
+            "pl7.app/vdj/feature": "FR2",
+            "alphabet": "aminoacid"
+          },
+          "annotations": {
+            "pl7.app/label": "FR2 aa"
+          }
+        }
+      }, {
+        "column": "aaSeqFR3",
+        "id": "aa-seq-fr3",
+        "spec": {
+          "valueType": "String",
+          "name": "pl7.app/vdj/sequence",
+          "domain": {
+            "pl7.app/vdj/feature": "FR3",
+            "alphabet": "aminoacid"
+          },
+          "annotations": {
+            "pl7.app/label": "FR3 aa"
+          }
+        }
+      }, {
+        "column": "aaSeqFR4",
+        "id": "aa-seq-fr4",
+        "spec": {
+          "valueType": "String",
+          "name": "pl7.app/vdj/sequence",
+          "domain": {
+            "pl7.app/vdj/feature": "FR4",
+            "alphabet": "aminoacid"
+          },
+          "annotations": {
+            "pl7.app/label": "FR4 aa"
+          }
+        }
+      }, {
+        "column": "aaSeqCDR1",
+        "id": "aa-seq-cdr1",
+        "spec": {
+          "valueType": "String",
+          "name": "pl7.app/vdj/sequence",
+          "domain": {
+            "pl7.app/vdj/feature": "CDR1",
+            "alphabet": "aminoacid"
+          },
+          "annotations": {
+            "pl7.app/label": "CDR1 aa"
+          }
+        }
+      }, {
+        "column": "aaSeqCDR2",
+        "id": "aa-seq-cdr2",
+        "spec": {
+          "valueType": "String",
+          "name": "pl7.app/vdj/sequence",
+          "domain": {
+            "pl7.app/vdj/feature": "CDR2",
+            "alphabet": "aminoacid"
+          },
+          "annotations": {
+            "pl7.app/label": "CDR2 aa"
+          }
+        }
+      }, {
+        "column": "aaSeqCDR3",
+        "id": "aa-seq-cdr3",
+        "spec": {
+          "valueType": "String",
+          "name": "pl7.app/vdj/sequence",
+          "domain": {
+            "pl7.app/vdj/feature": "CDR3",
+            "alphabet": "aminoacid"
+          },
+          "annotations": {
+            "pl7.app/label": "CDR3 aa"
+          }
+        }
+      }, {
+        "column": "nSeqImputedFR1",
+        "id": "n-seq-imputed-fr1",
+        "spec": {
+          "name": "pl7.app/vdj/sequence",
+          "valueType": "String",
+          "domain": {
+            "pl7.app/vdj/feature": "FR1",
+            "alphabet": "nucleotide"
+          },
+          "annotations": {
+            "pl7.app/label": "FR1 imputed nt"
+          }
+        }
+      }, {
+        "column": "nSeqImputedFR2",
+        "id": "n-seq-imputed-fr2",
+        "spec": {
+          "name": "pl7.app/vdj/sequence",
+          "valueType": "String",
+          "domain": {
+            "pl7.app/vdj/feature": "FR2",
+            "alphabet": "nucleotide"
+          },
+          "annotations": {
+            "pl7.app/label": "FR2 imputed nt"
+          }
+        }
+      }, {
+        "column": "nSeqImputedFR3",
+        "id": "n-seq-imputed-fr3",
+        "spec": {
+          "name": "pl7.app/vdj/sequence",
+          "valueType": "String",
+          "domain": {
+            "pl7.app/vdj/feature": "FR3",
+            "alphabet": "nucleotide"
+          },
+          "annotations": {
+            "pl7.app/label": "FR3 imputed nt"
+          }
+        }
+      }, {
+        "column": "nSeqImputedFR4",
+        "id": "n-seq-imputed-fr4",
+        "spec": {
+          "name": "pl7.app/vdj/sequence",
+          "valueType": "String",
+          "domain": {
+            "pl7.app/vdj/feature": "FR4",
+            "alphabet": "nucleotide"
+          },
+          "annotations": {
+            "pl7.app/label": "FR4 imputed nt"
+          }
+        }
+      }, {
+        "column": "nSeqImputedCDR1",
+        "id": "n-seq-imputed-cdr1",
+        "spec": {
+          "name": "pl7.app/vdj/sequence",
+          "valueType": "String",
+          "domain": {
+            "pl7.app/vdj/feature": "CDR1",
+            "alphabet": "nucleotide"
+          },
+          "annotations": {
+            "pl7.app/label": "CDR1 imputed nt"
+          }
+        }
+      }, {
+        "column": "nSeqImputedCDR2",
+        "id": "n-seq-imputed-cdr2",
+        "spec": {
+          "name": "pl7.app/vdj/sequence",
+          "valueType": "String",
+          "domain": {
+            "pl7.app/vdj/feature": "CDR2",
+            "alphabet": "nucleotide"
+          },
+          "annotations": {
+            "pl7.app/label": "CDR2 imputed nt"
+          }
+        }
+      }, {
+        "column": "nSeqImputedCDR3",
+        "id": "n-seq-imputed-CDR3",
+        "spec": {
+          "name": "pl7.app/vdj/sequence",
+          "valueType": "String",
+          "domain": {
+            "pl7.app/vdj/feature": "CDR3",
+            "alphabet": "nucleotide"
+          },
+          "annotations": {
+            "pl7.app/label": "CDR3 imputed nt"
+          }
+        }
+      }, {
+        "column": "aaSeqImputedFR1",
+        "id": "aa-seq-imputed-fr1",
+        "spec": {
+          "valueType": "String",
+          "name": "pl7.app/vdj/sequence",
+          "domain": {
+            "pl7.app/vdj/feature": "FR1",
+            "alphabet": "aminoacid"
+          },
+          "annotations": {
+            "pl7.app/label": "FR1 imputed aa"
+          }
+        }
+      }, {
+        "column": "aaSeqImputedFR2",
+        "id": "aa-seq-imputed-fr2",
+        "spec": {
+          "valueType": "String",
+          "name": "pl7.app/vdj/sequence",
+          "domain": {
+            "pl7.app/vdj/feature": "FR2",
+            "alphabet": "aminoacid"
+          },
+          "annotations": {
+            "pl7.app/label": "FR2 imputed aa"
+          }
+        }
+      }, {
+        "column": "aaSeqImputedFR3",
+        "id": "aa-seq-imputed-fr3",
+        "spec": {
+          "valueType": "String",
+          "name": "pl7.app/vdj/sequence",
+          "domain": {
+            "pl7.app/vdj/feature": "FR3",
+            "alphabet": "aminoacid"
+          },
+          "annotations": {
+            "pl7.app/label": "FR3 imputed aa"
+          }
+        }
+      }, {
+        "column": "aaSeqImputedFR4",
+        "id": "aa-seq-imputed-fr4",
+        "spec": {
+          "valueType": "String",
+          "name": "pl7.app/vdj/sequence",
+          "domain": {
+            "pl7.app/vdj/feature": "FR4",
+            "alphabet": "aminoacid"
+          },
+          "annotations": {
+            "pl7.app/label": "FR4 imputed aa"
+          }
+        }
+      }, {
+        "column": "aaSeqImputedCDR1",
+        "id": "aa-seq-imputed-cdr1",
+        "spec": {
+          "valueType": "String",
+          "name": "pl7.app/vdj/sequence",
+          "domain": {
+            "pl7.app/vdj/feature": "CDR1",
+            "alphabet": "aminoacid"
+          },
+          "annotations": {
+            "pl7.app/label": "CDR1 imputed aa"
+          }
+        }
+      }, {
+        "column": "aaSeqImputedCDR2",
+        "id": "aa-seq-imputed-cdr2",
+        "spec": {
+          "valueType": "String",
+          "name": "pl7.app/vdj/sequence",
+          "domain": {
+            "pl7.app/vdj/feature": "CDR2",
+            "alphabet": "aminoacid"
+          },
+          "annotations": {
+            "pl7.app/label": "CDR2 imputed aa"
+          }
+        }
+      }, {
+        "column": "aaSeqImputedCDR3",
+        "id": "aa-seq-imputed-CDR3",
+        "spec": {
+          "valueType": "String",
+          "name": "pl7.app/vdj/sequence",
+          "domain": {
+            "pl7.app/vdj/feature": "CDR3",
+            "alphabet": "aminoacid"
+          },
+          "annotations": {
+            "pl7.app/label": "CDR3 imputed aa"
+          }
+        }
+      }, {
+        "column": "isotype",
+        "id": "isotype",
+        "spec": {
+          "valueType": "String",
+          "name": "pl7.app/vdj/isotype",
+          "annotations": {
+            "pl7.app/label": "IG isotype"
+          }
+        }
+      }, {
+        "column": "topChains",
+        "id": "top-chains",
+        "allowNA": false,
+        "spec": {
+          "valueType": "String",
+          "name": "pl7.app/vdj/chain",
+          "annotations": {
+            "pl7.app/label": "Chain"
+          }
+        }
+      }
+      ],
+    "storageFormat": "Binary",
+    "partitionKeyLength": 0
+  }
 }
+
+export ll.toStrict({
+	getColumns: getColumns
+})
diff --git a/workflow/src/process.tpl.tengo b/workflow/src/process.tpl.tengo
index b054e42..92b7bf3 100644
--- a/workflow/src/process.tpl.tengo
+++ b/workflow/src/process.tpl.tengo
@@ -23,6 +23,9 @@ self.awaitState("pfconvParams", "ResourceReady")
 self.body(func(inputs) {
 	params := inputs.params
 	preset := params.preset
+	species := params.species
+	blockId := params.blockId
+
 	inputSpec := self.rawInputs().inputSpec.getValue().getDataAsJson()
 
 	presetContent := self.rawInputs().presetContent.getValue().getDataAsJson()
@@ -95,6 +98,7 @@ self.body(func(inputs) {
 		{
 			params: smart.createJsonResource({
 				preset: preset,
+				species: species,
 				fileExtension: fileExtension,
 				reports: reports
 			}),
@@ -113,6 +117,9 @@ self.body(func(inputs) {
 		"qc.spec": {
 			kind: "PColumn",
 			name: "mixcr.com/qc",
+			domain: {
+				"pl7.app/blockId": blockId
+			},
 			valueType: "File",
 			axesSpec: [
 				inputSpec.axesSpec[0]
@@ -123,6 +130,9 @@ self.body(func(inputs) {
 		"logs.spec": {
 			kind: "PColumn",
 			name: "pl7.app/log",
+			domain: {
+				"pl7.app/blockId": blockId
+			},
 			valueType: "Log",
 			axesSpec: [
 				inputSpec.axesSpec[0]
@@ -133,6 +143,9 @@ self.body(func(inputs) {
 		"reports.spec": {
 			kind: "PColumn",
 			name: "mixcr.com/report",
+			domain: {
+				"pl7.app/blockId": blockId
+			},
 			valueType: "File",
 			axesSpec: [
 				inputSpec.axesSpec[0],
@@ -157,6 +170,15 @@ self.body(func(inputs) {
 		},
 		"reports.data": mixcrResults.output("reports"),
 
+		"clns.spec": {
+			kind: "PColumn",
+			name: "mixcr.com/clns",
+			domain: {
+				"pl7.app/blockId": blockId
+			},
+			valueType: "File",
+			axesSpec: [ inputSpec.axesSpec[0] ]
+		},
 		"clns.data": mixcrResults.output("clns"),
 
 		"clones": clones.lockAndBuild()