@platforma-open/milaboratories.tcrdisco-enrichment.workflow 1.1.0

package/.turbo/turbo-build.log

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+ WARN  Issue while reading "/home/runner/work/tcr-disco/tcr-disco/.npmrc". Failed to replace env in config: ${NPMJS_TOKEN}
+
+> @platforma-open/milaboratories.tcrdisco-enrichment.workflow@1.1.0 build /home/runner/work/tcr-disco/tcr-disco/workflow
+> rm -rf dist && pl-tengo check && pl-tengo build
+
+  info: Skipping unknown file type: wf.test.ts
+Processing "src/libs/cd_subset_params.lib.tengo"...
+Processing "src/libs/tcr_pairs_params.lib.tengo"...
+Processing "src/libs/tcrdisco_da_pfconv_params.lib.tengo"...
+Processing "src/libs/top_frequencies.lib.tengo"...
+Processing "src/libs/top_table_pfconv_params.lib.tengo"...
+Processing "src/main.tpl.tengo"...
+Processing "src/tcr-ab-pairs.tpl.tengo"...
+Processing "src/tcr-analysis.tpl.tengo"...
+No syntax errors found.
+  info: Skipping unknown file type: wf.test.ts
+  info: Compiling 'dist'...
+  info:   - writing /home/runner/work/tcr-disco/tcr-disco/workflow/dist/tengo/lib/libs.cd_subset_params.lib.tengo
+  info:   - writing /home/runner/work/tcr-disco/tcr-disco/workflow/dist/tengo/lib/libs.tcr_pairs_params.lib.tengo
+  info:   - writing /home/runner/work/tcr-disco/tcr-disco/workflow/dist/tengo/lib/libs.tcrdisco_da_pfconv_params.lib.tengo
+  info:   - writing /home/runner/work/tcr-disco/tcr-disco/workflow/dist/tengo/lib/libs.top_frequencies.lib.tengo
+  info:   - writing /home/runner/work/tcr-disco/tcr-disco/workflow/dist/tengo/lib/libs.top_table_pfconv_params.lib.tengo
+  info:   - writing /home/runner/work/tcr-disco/tcr-disco/workflow/dist/tengo/tpl/tcr-ab-pairs.plj.gz
+  info:   - writing /home/runner/work/tcr-disco/tcr-disco/workflow/dist/tengo/tpl/tcr-analysis.plj.gz
+  info:   - writing /home/runner/work/tcr-disco/tcr-disco/workflow/dist/tengo/tpl/main.plj.gz
+  info: Template Pack build done.
+  info: Template Pack build done.

package/CHANGELOG.md

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+# @platforma-open/milaboratories.tcrdisco-enrichment.workflow
+
+## 1.1.0
+
+### Minor Changes
+
+- ede2472: First block version
+
+### Patch Changes
+
+- Updated dependencies [ede2472]
+  - @platforma-open/milaboratories.run-tcrdisco-enrichment.software@1.1.0

package/dist/index.cjs

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+module.exports = { Templates: {
+  'tcr-ab-pairs': { type: 'from-file', path: require.resolve('./tengo/tpl/tcr-ab-pairs.plj.gz') },
+  'tcr-analysis': { type: 'from-file', path: require.resolve('./tengo/tpl/tcr-analysis.plj.gz') },
+  'main': { type: 'from-file', path: require.resolve('./tengo/tpl/main.plj.gz') }
+}};

package/dist/index.d.ts

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+declare type TemplateFromFile = { readonly type: "from-file"; readonly path: string; };
+declare type TplName = "tcr-ab-pairs" | "tcr-analysis" | "main";
+declare const Templates: Record<TplName, TemplateFromFile>;
+export { Templates };

package/dist/index.js

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+import { resolve } from 'node:path';
+export const Templates = {
+  'tcr-ab-pairs': { type: 'from-file', path: resolve(import.meta.dirname, './tengo/tpl/tcr-ab-pairs.plj.gz') },
+  'tcr-analysis': { type: 'from-file', path: resolve(import.meta.dirname, './tengo/tpl/tcr-analysis.plj.gz') },
+  'main': { type: 'from-file', path: resolve(import.meta.dirname, './tengo/tpl/main.plj.gz') }
+};

package/dist/tengo/lib/libs.cd_subset_params.lib.tengo

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+ll := import("@platforma-sdk/workflow-tengo:ll")
+
+getColumns := func(countsSpec) {
+	field := "differentialTCRAbundance"
+	degName := "log2foldchange"
+
+	axes := [
+			{
+				column: "clonotypeKey",
+				spec: countsSpec.axesSpec[1]
+			}
+			]
+
+	columns := [
+			{
+				column: "subset",
+				id: "subset",
+				allowNA: true,
+				spec: {
+					name: "pl7.app/" + field + "/subset",
+					valueType: "String",
+					annotations: {
+						"pl7.app/label": "CD4/CD8 subset",
+						"pl7.app/table/visibility": "default",
+						"pl7.app/table/orderPriority": "60"
+					}
+				}
+			}
+			]
+
+	return {
+		axes: axes,
+		columns: columns,
+		"storageFormat": "Parquet",
+		"partitionKeyLength": 0
+	}
+}
+
+export ll.toStrict({
+	getColumns: getColumns
+})
+

package/dist/tengo/lib/libs.tcr_pairs_params.lib.tengo

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+ll := import("@platforma-sdk/workflow-tengo:ll")
+math := import("math")
+
+getColumns := func(countsSpecAlpha, countsSpecBeta) {
+	field := "differentialTCRAbundance"
+	degName := "log2foldchange"
+
+	axes := [
+			{
+				column: "Numerator",
+				id: "numerator",
+				allowNA: false,
+				spec: {
+					name: "pl7.app/" + field + "/numerator",
+					type: "String",
+					annotations: {
+						"pl7.app/label": "Numerator"
+					}
+				}
+			},
+			{
+				column: "tra",
+				spec: countsSpecAlpha.axesSpec[1]
+			},
+			{
+				column: "trb",
+				spec: countsSpecBeta.axesSpec[1]
+			}
+			]
+
+	columns := [
+			{
+				column: "estimate",
+				id: "estimate",
+				allowNA: true,
+				spec: {
+					name: "pl7.app/" + field + "/estimate",
+					valueType: "Double",
+					annotations: {
+						"pl7.app/label": "Correlation",
+						"pl7.app/table/orderPriority": "70",
+						"pl7.app/min":"0",
+            			"pl7.app/max": "1",
+						"pl7.app/table/visibility": "default"
+					}
+				}
+			},
+			{
+				column: "p.value",
+				id: "pvalue",
+				allowNA: true,
+				spec: {
+					name: "pl7.app/" + field + "/pvalue",
+					valueType: "Double",
+					annotations: {
+						"pl7.app/label": "P-value",
+						"pl7.app/table/orderPriority": "60",
+						"pl7.app/graph/axis/symmetricRange": "0",
+						"pl7.app/table/visibility": "optional"
+					}
+				}
+			},
+			{
+				column: "p.adj",
+				id: "padj",
+				allowNA: true,
+				spec: {
+					name: "pl7.app/" + field + "/padj",
+					valueType: "Double",
+					annotations: {
+						"pl7.app/label": "Adjusted p-value",
+						"pl7.app/table/orderPriority": "50",
+						"pl7.app/table/visibility": "default"
+					}
+				}
+			},
+			{
+				column: "tra_CDR3aa",
+				id: "tra_CDR3aa",
+				allowNA: true,
+				spec: {
+					name: "pl7.app/" + field + "/tra_CDR3aa",
+					valueType: "String",
+					annotations: {
+						"pl7.app/label": "TCR Alpha CDR3 aa",
+						"pl7.app/table/orderPriority": "40",
+						"pl7.app/table/visibility": "default"
+					}
+				}
+			},
+			{
+				column: "trb_CDR3aa",
+				id: "trb_CDR3aa",
+				allowNA: true,
+				spec: {
+					name: "pl7.app/" + field + "/trb_CDR3aa",
+					valueType: "String",
+					annotations: {
+						"pl7.app/label": "TCR Beta CDR3 aa",
+						"pl7.app/table/orderPriority": "30",
+						"pl7.app/table/visibility": "default"
+					}
+				}
+			},
+			{
+				column: "tra_VGene",
+				id: "tra_VGene",
+				allowNA: true,
+				spec: {
+					name: "pl7.app/" + field + "/tra_VGene",
+					valueType: "String",
+					annotations: {
+						"pl7.app/label": "TCR Alpha VGene",
+						"pl7.app/table/orderPriority": "20",
+						"pl7.app/table/visibility": "optional"
+					}
+				}
+			},
+			{
+				column: "trb_VGene",
+				id: "trb_VGene",
+				allowNA: true,
+				spec: {
+					name: "pl7.app/" + field + "/trb_VGene",
+					valueType: "String",
+					annotations: {
+						"pl7.app/label": "TCR Beta VGene",
+						"pl7.app/table/orderPriority": "10",
+						"pl7.app/table/visibility": "optional"
+					}
+				}
+			},
+			{
+				column: "is_max_correlation",
+				id: "is_max_correlation",
+				allowNA: true,
+				spec: {
+					name: "pl7.app/" + field + "/max_cc_info",
+					valueType: "String",
+					annotations: {
+						"pl7.app/label": "Maximum correlation",
+						"pl7.app/table/orderPriority": "5",
+						"pl7.app/table/visibility": "optional"
+					}
+				}
+			}
+			]
+
+	return {
+		axes: axes,
+		columns: columns,
+		"storageFormat": "Parquet",
+		"partitionKeyLength": 1
+	}
+}
+
+export ll.toStrict({
+	getColumns: getColumns
+})

package/dist/tengo/lib/libs.tcrdisco_da_pfconv_params.lib.tengo

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+ll := import("@platforma-sdk/workflow-tengo:ll")
+json := import("json")
+
+getColumns := func(countsSpec, cdSubsetCol, numerator, comparison) {
+
+
+	runIdLabel := countsSpec.axesSpec[1].domain["pl7.app/vdj/clonotypingRunId"]
+	if runIdLabel == undefined {
+		runIdLabel = "pl7.app/vdj/vdjImport"
+	} else {
+		runIdLabel = "pl7.app/vdj/clonotypingRunId"
+	}
+
+	columns := [
+			{
+				column: "Robust_Enrichment",
+				id: "robustEnrichment",
+				allowNA: true,
+				spec: {
+					name: "pl7.app/differentialTCRAbundance/robustEnrichment",
+					valueType: "String",
+					annotations: {
+						"pl7.app/label": "Robust enrichment - " + numerator,
+						"pl7.app/table/visibility": "optional",
+						"pl7.app/table/orderPriority": "84000",
+						"pl7.app/hideDataFromGraphs": "true",
+						"pl7.app/isDiscreteFilter": "true",
+						"pl7.app/discreteValues": string(json.encode(["Robust", "Non-robust"]))
+					},
+					domain: {
+						runIdLabel: countsSpec.axesSpec[1].domain[runIdLabel],
+						"pl7.app/differentialTCRAbundance/comparison": comparison
+					}
+				}
+			}
+			]
+
+	return {
+		"axes": [
+			{
+				column: "clonotypeKey",
+				spec: countsSpec.axesSpec[1]
+			}
+			],
+		"columns": columns,
+		"storageFormat": "Parquet",
+		"partitionKeyLength": 0
+	}
+}
+
+export ll.toStrict({
+	getColumns: getColumns
+})
+

package/dist/tengo/lib/libs.top_frequencies.lib.tengo

@@ -0,0 +1,46 @@
+ll := import("@platforma-sdk/workflow-tengo:ll")
+math := import("math")
+
+getColumns := func(countsSpec) {
+	field := "differentialTCRAbundance"
+	degName := "log2foldchange"
+
+	axes := [
+			{
+				column: "internalSampleId",
+				spec: countsSpec.axesSpec[0]
+			},
+			{
+				column: "clonotypeKey",
+				spec: countsSpec.axesSpec[1]
+			}
+			]
+
+	columns := [
+			{
+				column: "fraction",
+				id: "fraction",
+				allowNA: true,
+				spec: {
+					name: "pl7.app/" + field + "/countFraction",
+					valueType: "Double",
+					annotations: {
+						"pl7.app/label": "Fraction of counts",
+						"pl7.app/table/orderPriority": "100",
+						"pl7.app/table/visibility": "default"
+					}
+				}
+			}
+			]
+
+	return {
+		axes: axes,
+		columns: columns,
+		"storageFormat": "Parquet",
+		"partitionKeyLength": 1
+	}
+}
+
+export ll.toStrict({
+	getColumns: getColumns
+})

package/dist/tengo/lib/libs.top_table_pfconv_params.lib.tengo

@@ -0,0 +1,238 @@
+ll := import("@platforma-sdk/workflow-tengo:ll")
+math := import("math")
+
+getColumns := func(countsSpec, inputType, log2FCThreshold, pAdjFCThreshold, cdSubsetCol, denominators) {
+	field := "differentialTCRAbundance"
+
+
+	thresholds := "[{\"columnId\": {\"name\": \"pl7.app/" + field + "/log2foldchange_mean\",\"valueType\": \"Double\"},\"label\": \"Min LogFC (left vertical)\",\"value\": " + string(-log2FCThreshold) + "},"
+	thresholds = thresholds + "{\"columnId\": {\"name\": \"pl7.app/" + field + "/log2foldchange_mean\",\"valueType\": \"Double\"},\"label\": \"Max LogFC (right vertical)\",\"value\": " + string(log2FCThreshold) + "},"
+	thresholds = thresholds + "{\"columnId\": {\"name\": \"pl7.app/" + field + "/minlog10padj_mean\",\"valueType\": \"Double\"},\"label\": \"Y bound\",\"value\": " + string(-math.log10(pAdjFCThreshold)) + "}]"
+	
+
+	axes := [
+			{
+				column: "Contrast",
+				id: "contrast",
+				allowNA: false,
+				spec: {
+					name: "pl7.app/" + field + "/contrastGroup",
+					type: "String",
+					annotations: {
+						"pl7.app/label": "Contrast"
+					}
+				}
+			},
+			{
+				column: "clonotypeKey",
+				spec: countsSpec.axesSpec[1]
+			}
+			]
+
+	columns := [
+			{
+				column: "CDR3aa",
+				id: "cdr3aa",
+				allowNA: true,
+				spec: {
+					name: "pl7.app/" + field + "/cdr3aa",
+					valueType: "String",
+					annotations: {
+						"pl7.app/label": "CDR3 aa",
+						"pl7.app/table/orderPriority": "200",
+						"pl7.app/table/visibility": "default"
+					}
+				}
+			},
+			{
+				column: "VGene",
+				id: "vgene",
+				allowNA: true,
+				spec: {
+					name: "pl7.app/" + field + "/vgene",
+					valueType: "String",
+					annotations: {
+						"pl7.app/label": "VGene",
+						"pl7.app/table/orderPriority": "195",
+						"pl7.app/table/visibility": "default"
+					}
+				}
+			},
+			{
+				column: "log2FoldChange",
+				id: "log2foldchange",
+				allowNA: true,
+				spec: {
+					name: "pl7.app/" + field + "/log2foldchange",
+					valueType: "Double",
+					annotations: {
+						"pl7.app/label": "Log2FC",
+						"pl7.app/table/orderPriority": "95",
+						"pl7.app/graph/axis/symmetricRange": "0",
+						"pl7.app/table/visibility": "default"
+					}
+				}
+			},
+			{
+				column: "pvalue",
+				id: "pvalue",
+				allowNA: true,
+				spec: {
+					name: "pl7.app/" + field + "/pvalue",
+					valueType: "Double",
+					annotations: {
+						"pl7.app/label": "P-value",
+						"pl7.app/table/orderPriority": "110",
+						"pl7.app/table/visibility": "optional"
+					}
+				}
+			},
+			{
+				column: "padj",
+				id: "padj",
+				allowNA: true,
+				spec: {
+					name: "pl7.app/" + field + "/padj",
+					valueType: "Double",
+					annotations: {
+						"pl7.app/label": "Adjusted p-value",
+						"pl7.app/table/orderPriority": "105",
+						"pl7.app/table/visibility": "default"
+					}
+				}
+			},
+			{
+				column: "minlog10padj",
+				id: "minlog10padj",
+				allowNA: true,
+				spec: {
+					name: "pl7.app/" + field + "/minlog10padj",
+					valueType: "Double",
+					annotations: {
+						"pl7.app/label": "-log10 adjusted p-value",
+						"pl7.app/table/orderPriority": "100",
+						"pl7.app/table/visibility": "optional"
+					}
+				}
+			},
+			{
+				column: "Regulation",
+				id: "regulationDirection",
+				spec: {
+					name: "pl7.app/" + field + "/regulationDirection",
+					valueType: "String",
+					annotations: {
+						"pl7.app/label": "Regulation direction",
+						"pl7.app/graph/palette": "{\"name\":\"triadic\",\"mapping\":{\"Up\":\"19\",\"Down\":\"22\",\"NS\":\"25\"}}",
+						"pl7.app/graph/thresholds": thresholds,
+						"pl7.app/table/orderPriority": "80",
+						"pl7.app/table/visibility": "optional"
+					}
+				}
+			},
+			{
+				column: "Robust_Enrichment",
+				id: "robustEnrichment",
+				spec: {
+					name: "pl7.app/" + field + "/robustEnrichment",
+					valueType: "String",
+					annotations: {
+						"pl7.app/label": "Robust enrichment",
+						"pl7.app/table/orderPriority": "155",
+						"pl7.app/table/visibility": "optional"
+					}
+				}
+			}
+			]
+	if cdSubsetCol != undefined {
+		columns += [{
+				column: "subset",
+				id: "subset",
+				spec: {
+					name: "pl7.app/" + field + "/cdsubset",
+					valueType: "String",
+					annotations: {
+						"pl7.app/label": "CD4/CD8 subset",
+						"pl7.app/table/visibility": "default",
+						"pl7.app/table/orderPriority": "150"
+					}
+				}
+			},
+			{
+				column: "umi_count_CD4",
+				id: "umi_count_CD4",
+				spec: {
+					name: "pl7.app/" + field + "/umi_count_CD4",
+					valueType: "Double",
+					annotations: {
+						"pl7.app/label": "UMI count CD4",
+						"pl7.app/table/visibility": "optional",
+						"pl7.app/table/orderPriority": "145"
+					}
+				}
+			},
+			{
+				column: "umi_freq_CD4",
+				id: "umi_freq_CD4",
+				spec: {
+					name: "pl7.app/" + field + "/umi_freq_CD4",
+					valueType: "Double",
+					annotations: {
+						"pl7.app/label": "UMI frequency CD4",
+						"pl7.app/table/visibility": "optional",
+						"pl7.app/table/orderPriority": "140"
+					}
+				}
+			},
+			{
+				column: "umi_count_CD8",
+				id: "umi_count_CD8",
+				spec: {
+					name: "pl7.app/" + field + "/umi_count_CD8",
+					valueType: "Double",
+					annotations: {
+						"pl7.app/label": "UMI count CD8",
+						"pl7.app/table/visibility": "optional",
+						"pl7.app/table/orderPriority": "135"
+					}
+				}
+			},
+			{
+				column: "umi_freq_CD8",
+				id: "umi_freq_CD8",
+				spec: {
+					name: "pl7.app/" + field + "/umi_freq_CD8",
+					valueType: "Double",
+					annotations: {
+						"pl7.app/label": "UMI frequency CD8",
+						"pl7.app/table/visibility": "optional",
+						"pl7.app/table/orderPriority": "130"
+					}
+				}
+			},
+			{
+				column: "subset_frequency",
+				id: "subset_frequency",
+				spec: {
+					name: "pl7.app/" + field + "/cdsubset_frequency",
+					valueType: "Double",
+					annotations: {
+						"pl7.app/label": "Log(10) major subset frequency",
+						"pl7.app/table/visibility": "optional",
+						"pl7.app/table/orderPriority": "125"
+					}
+				}
+			}]
+	}
+			
+	return {
+		axes: axes,
+		columns: columns,
+		"storageFormat": "Parquet",
+		"partitionKeyLength": 1
+	}
+}
+
+export ll.toStrict({
+	getColumns: getColumns
+})

package/format.el

@@ -0,0 +1,43 @@
+;; This program formats all files inside src directory. Usage: emacs --script ./format.el
+
+(defun install-go-mode ()
+  "Installs go-mode"
+  (require 'package)
+  (add-to-list 'package-archives
+               '("melpa-stable" . "https://stable.melpa.org/packages/"))
+  (package-initialize)
+  (unless package-archive-contents
+    (package-refresh-contents))
+
+  (package-install 'go-mode t)
+  (require 'go-mode))
+
+;; spaces -> tabs only at the beginning of lines
+(setq tabify-regexp "^\t* [ \t]+")
+
+(defun format-file (file)
+  "Formats a file according to slightly changed Go rules"
+  (message "Format %s" file)
+  (save-excursion
+    (find-file file)
+    (delete-trailing-whitespace)            ;; deletes whitespaces
+    (go-mode)                               ;; sets golang rules for indentation
+    (tabify (point-min) (point-max))        ;; spaces -> tabs in the whole file
+    (indent-region (point-min) (point-max)) ;; indentation in the whole file
+    (save-buffer)))                         ;; save file
+
+(install-go-mode)
+
+;; change syntax of a standard go-mode a bit
+(advice-add
+ 'go--in-composite-literal-p
+ :filter-return
+ (lambda (&rest r) t))
+
+;; find all files in src
+(setq files (directory-files-recursively "src" "\\.tengo\\'"))
+
+;; call format on every file.
+(dolist (file files)
+  (format-file file))
+

package/index.d.ts

@@ -0,0 +1,4 @@
+declare type TemplateFromFile = { readonly type: "from-file"; readonly path: string; };
+declare type TplName = "main";
+declare const Templates: Record<TplName, TemplateFromFile>;
+export { Templates };

package/index.js

@@ -0,0 +1,3 @@
+module.exports = { Templates: {
+  'main': { type: 'from-file', path: require.resolve('./dist/tengo/tpl/main.plj.gz') }
+}}

package/package.json

@@ -0,0 +1,20 @@
+{
+  "name": "@platforma-open/milaboratories.tcrdisco-enrichment.workflow",
+  "version": "1.1.0",
+  "type": "module",
+  "description": "Block Workflow",
+  "dependencies": {
+    "@platforma-sdk/workflow-tengo": "^5.6.4",
+    "@platforma-open/milaboratories.run-tcrdisco-enrichment.software": "1.1.0"
+  },
+  "devDependencies": {
+    "@platforma-sdk/tengo-builder": "^2.3.14",
+    "@platforma-sdk/test": "^1.46.3",
+    "vitest": "~2.1.9"
+  },
+  "scripts": {
+    "build": "rm -rf dist && pl-tengo check && pl-tengo build",
+    "test": "vitest",
+    "format": "/usr/bin/env emacs --script ./format.el"
+  }
+}