@platforma-open/milaboratories.mixcr-amplicon-alignment.workflow 1.0.1 → 1.2.0

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Files changed (13) hide show
  1. package/.turbo/turbo-build.log +1 -1
  2. package/CHANGELOG.md +12 -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 +1 -1
  10. package/src/main.tpl.tengo +2 -0
  11. package/src/mixcr-analyze.tpl.tengo +22 -13
  12. package/src/mixcr-export.tpl.tengo +2 -2
  13. package/src/process.tpl.tengo +4 -4
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@1.0.1 build /home/runner/work/mixcr-amplicon-alignment/mixcr-amplicon-alignment/workflow
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+ > @platforma-open/milaboratories.mixcr-amplicon-alignment.workflow@1.2.0 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 +1,17 @@
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  # @platforma-open/milaboratories.mixcr-amplicon-alignment.workflow
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+ ## 1.2.0
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+
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+ ### Minor Changes
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+
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+ - 86528bc: add only productive option to mixcr export
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+
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+ ## 1.1.0
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+
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+ ### Minor Changes
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+
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+ - 2ac7c87: Wildcards in reference sequence and --limit-input option in MiXCR
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+
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  ## 1.0.1
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  ### Patch 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
Binary file
package/package.json CHANGED
@@ -1,6 +1,6 @@
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  {
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  "name": "@platforma-open/milaboratories.mixcr-amplicon-alignment.workflow",
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- "version": "1.0.1",
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+ "version": "1.2.0",
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  "description": "MiXCR Amplicon Alignment Workflow",
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  "type": "module",
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  "dependencies": {
package/src/main.tpl.tengo CHANGED
@@ -29,6 +29,7 @@ wf.body(func(args) {
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  threePrimePrimer := args.threePrimePrimer
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  fivePrimePrimer := args.fivePrimePrimer
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  chains := args.chains
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+ limitInput := args.limitInput
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  // Create V and J gene FASTA files
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@@ -76,6 +77,7 @@ wf.body(func(args) {
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  inputSpec: input.getFutureInputField("spec"),
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  inputData: input.getFutureInputField("data"),
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  referenceLibrary: referenceLibrary,
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+ limitInput: limitInput,
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  params: smart.createJsonResource({
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  blockId: blockId,
package/src/mixcr-analyze.tpl.tengo CHANGED
@@ -26,6 +26,9 @@ self.body(func(inputs) {
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  params := inputs.params
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  fileExtension := params.fileExtension
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+ limitInput := inputs.limitInput
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+ ll.print("__THE_LOG__" + string(limitInput))
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+
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  threePrimePrimer := inputs.threePrimePrimer
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  fivePrimePrimer := inputs.fivePrimePrimer
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@@ -59,19 +62,25 @@ self.body(func(inputs) {
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  arg("--library").arg("library.json").
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  addFile("library.json", params.referenceLibrary).
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  arg("--rna").
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- arg("--force-overwrite")
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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 {
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- mixcrCmdBuilder.arg("--rigid-left-alignment-boundary")
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- }
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-
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- if (!is_undefined(fivePrimePrimer)) {
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- mixcrCmdBuilder.arg("--floating-right-alignment-boundary").arg("J")
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- } else {
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- mixcrCmdBuilder.arg("--rigid-right-alignment-boundary").arg("J")
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- }
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+ arg("--force-overwrite").
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+ arg("--rigid-left-alignment-boundary").
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+ arg("--rigid-right-alignment-boundary").arg("J")
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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 {
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+ // mixcrCmdBuilder.arg("--rigid-left-alignment-boundary")
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+ // }
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+
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+ // if (!is_undefined(fivePrimePrimer)) {
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+ // mixcrCmdBuilder.arg("--floating-right-alignment-boundary").arg("J")
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+ // } else {
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+ // mixcrCmdBuilder.arg("--rigid-right-alignment-boundary").arg("J")
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+ // }
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+
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+ if !is_undefined(limitInput) {
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+ mixcrCmdBuilder.arg("--limit-input").arg(string(limitInput))
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+ }
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  // Handle input files
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  inputMap := inputData.inputs()
package/src/mixcr-export.tpl.tengo CHANGED
@@ -40,8 +40,8 @@ self.body(func(inputs) {
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  arg("--dont-split-files").
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  arg("--drop-default-fields").
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  arg("--reset-export-clone-table-splitting").
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- arg("--chains").arg(params.mixcrChains)
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- //arg("--export-productive-clones-only")
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+ arg("--chains").arg(params.mixcrChains).
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+ arg("--export-productive-clones-only")
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  additionalAction(mixcrCmdBuilder)
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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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+ limitInput := inputs.limitInput
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  fileExtension := inputSpec.domain["pl7.app/fileExtension"]
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  // Use calculateExportSpecs for output columns
@@ -158,10 +159,9 @@ self.body(func(inputs) {
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  params: {
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  fileExtension: fileExtension,
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  referenceLibrary: referenceLibrary
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- }
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- },
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- threePrimePrimer: threePrimePrimer,
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- fivePrimePrimer: fivePrimePrimer
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+ },
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+ limitInput: limitInput
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+ }
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  }
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  )
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