@platforma-open/milaboratories.mixcr-amplicon-alignment.workflow 1.5.0 → 1.7.0

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Files changed (13) hide show
  1. package/.turbo/turbo-build.log +1 -1
  2. package/CHANGELOG.md +13 -0
  3. package/dist/tengo/tpl/aggregate-by-clonotype-key.plj.gz +0 -0
  4. package/dist/tengo/tpl/main.plj.gz +0 -0
  5. package/dist/tengo/tpl/mixcr-analyze.plj.gz +0 -0
  6. package/dist/tengo/tpl/mixcr-export.plj.gz +0 -0
  7. package/dist/tengo/tpl/process.plj.gz +0 -0
  8. package/dist/tengo/tpl/repseqio-library.plj.gz +0 -0
  9. package/package.json +4 -4
  10. package/src/main.tpl.tengo +3 -1
  11. package/src/mixcr-analyze.tpl.tengo +8 -0
  12. package/src/mixcr-export.tpl.tengo +0 -1
  13. package/src/process.tpl.tengo +3 -1
package/.turbo/turbo-build.log CHANGED
@@ -1,6 +1,6 @@
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   WARN  Issue while reading "/home/runner/work/mixcr-amplicon-alignment/mixcr-amplicon-alignment/.npmrc". Failed to replace env in config: ${NPMJS_TOKEN}
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- > @platforma-open/milaboratories.mixcr-amplicon-alignment.workflow@1.5.0 build /home/runner/work/mixcr-amplicon-alignment/mixcr-amplicon-alignment/workflow
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+ > @platforma-open/milaboratories.mixcr-amplicon-alignment.workflow@1.7.0 build /home/runner/work/mixcr-amplicon-alignment/mixcr-amplicon-alignment/workflow
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  > rm -rf dist && pl-tengo check && pl-tengo build
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  info: Skipping unknown file type: wf.test.ts
package/CHANGELOG.md CHANGED
@@ -1,5 +1,18 @@
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  # @platforma-open/milaboratories.mixcr-amplicon-alignment.workflow
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+ ## 1.7.0
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+
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+ ### Minor Changes
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+
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+ - 3b008c0: speed up MiXCR clustering by relaxing fuzzy matching criteria or turning of clustering itself
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+ - 3b008c0: updating SDK
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+
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+ ## 1.6.0
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+
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+ ### Minor Changes
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+
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+ - 2af4406: Removed unused software import
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+
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  ## 1.5.0
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  ### Minor Changes
package/dist/tengo/tpl/main.plj.gz CHANGED
Binary file
package/dist/tengo/tpl/mixcr-analyze.plj.gz CHANGED
Binary file
package/dist/tengo/tpl/mixcr-export.plj.gz CHANGED
Binary file
package/dist/tengo/tpl/process.plj.gz CHANGED
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package/package.json CHANGED
@@ -1,16 +1,16 @@
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  {
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  "name": "@platforma-open/milaboratories.mixcr-amplicon-alignment.workflow",
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- "version": "1.5.0",
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+ "version": "1.7.0",
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  "description": "MiXCR Amplicon Alignment Workflow",
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  "type": "module",
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  "dependencies": {
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- "@platforma-sdk/workflow-tengo": "^4.9.2",
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+ "@platforma-sdk/workflow-tengo": "^5.2.0",
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  "@platforma-open/milaboratories.software-mixcr": "4.7.0-169-develop",
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  "@platforma-open/milaboratories.software-repseqio": "^2.5.0-13-master"
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  },
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  "devDependencies": {
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- "@platforma-sdk/tengo-builder": "^2.1.12",
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- "@platforma-sdk/test": "^1.38.0",
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+ "@platforma-sdk/tengo-builder": "^2.1.19",
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+ "@platforma-sdk/test": "^1.43.0",
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  "vitest": "^2.1.8"
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  },
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  "scripts": {
package/src/main.tpl.tengo CHANGED
@@ -32,6 +32,7 @@ wf.body(func(args) {
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  limitInput := args.limitInput
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  perProcessMemGB := args.perProcessMemGB
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  perProcessCPUs := args.perProcessCPUs
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+ cloneClusteringMode := args.cloneClusteringMode
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  // Create V and J gene FASTA files
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@@ -88,7 +89,8 @@ wf.body(func(args) {
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  threePrimePrimer: threePrimePrimer,
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  fivePrimePrimer: fivePrimePrimer,
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  chains: chains,
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- mixcrChains: chainInfos[chains].mixcrFilter
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+ mixcrChains: chainInfos[chains].mixcrFilter,
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+ cloneClusteringMode: cloneClusteringMode
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  })
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  })
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package/src/mixcr-analyze.tpl.tengo CHANGED
@@ -29,6 +29,7 @@ self.body(func(inputs) {
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  limitInput := inputs.limitInput
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  perProcessMemGB := inputs.perProcessMemGB
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  perProcessCPUs := inputs.perProcessCPUs
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+ cloneClusteringMode := params.cloneClusteringMode
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  ll.print("__THE_LOG__" + string(limitInput))
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  threePrimePrimer := inputs.threePrimePrimer
@@ -68,6 +69,13 @@ self.body(func(inputs) {
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  arg("--rigid-left-alignment-boundary").
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  arg("--rigid-right-alignment-boundary").arg("J")
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+ // Clone clustering tuning
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+ if cloneClusteringMode == "decrease" {
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+ mixcrCmdBuilder.arg("-Massemble.cloneAssemblerParameters.cloneClusteringParameters.searchParameters=oneMismatchOrIndel")
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+ } else if cloneClusteringMode == "off" {
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+ mixcrCmdBuilder.arg("-Massemble.cloneAssemblerParameters.cloneClusteringParameters=null")
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+ }
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+
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  // if (!is_undefined(threePrimePrimer)) {
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  // mixcrCmdBuilder.arg("--floating-left-alignment-boundary")
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  // } else {
package/src/mixcr-export.tpl.tengo CHANGED
@@ -10,7 +10,6 @@ pt := import("@platforma-sdk/workflow-tengo:pt")
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  json := import("json")
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  mixcrSw := assets.importSoftware("@platforma-open/milaboratories.software-mixcr:main")
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- ptablerSw := assets.importSoftware("@platforma-open/milaboratories.software-ptabler:main")
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  self.defineOutputs("tsv")
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package/src/process.tpl.tengo CHANGED
@@ -31,6 +31,7 @@ self.body(func(inputs) {
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  fivePrimePrimer := params.fivePrimePrimer
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  chains := params.chains
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  mixcrChains := params.mixcrChains
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+ cloneClusteringMode := params.cloneClusteringMode
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  limitInput := inputs.limitInput
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  perProcessMemGB := params.perProcessMemGB
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  perProcessCPUs := params.perProcessCPUs
@@ -160,7 +161,8 @@ self.body(func(inputs) {
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  extra: {
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  params: {
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  fileExtension: fileExtension,
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- referenceLibrary: referenceLibrary
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+ referenceLibrary: referenceLibrary,
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+ cloneClusteringMode: cloneClusteringMode
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  },
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  limitInput: limitInput
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  },