@platforma-open/milaboratories.mixcr-amplicon-alignment.workflow 1.21.7 → 1.21.9

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Files changed (12) 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/export-report.plj.gz +0 -0
  5. package/dist/tengo/tpl/main.plj.gz +0 -0
  6. package/dist/tengo/tpl/mixcr-analyze.plj.gz +0 -0
  7. package/dist/tengo/tpl/mixcr-export.plj.gz +0 -0
  8. package/dist/tengo/tpl/prerun.plj.gz +0 -0
  9. package/dist/tengo/tpl/process.plj.gz +0 -0
  10. package/dist/tengo/tpl/repseqio-library.plj.gz +0 -0
  11. package/package.json +2 -2
  12. package/src/repseqio-library.tpl.tengo +9 -9
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@1.21.7 build /home/runner/work/mixcr-amplicon-alignment/mixcr-amplicon-alignment/workflow
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+ > @platforma-open/milaboratories.mixcr-amplicon-alignment.workflow@1.21.9 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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  Processing "src/aggregate-by-clonotype-key.tpl.tengo"...
package/CHANGELOG.md CHANGED
@@ -1,5 +1,17 @@
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  # @platforma-open/milaboratories.mixcr-amplicon-alignment.workflow
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+ ## 1.21.9
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+
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+ ### Patch Changes
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+
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+ - b3d0382: Fix `FileNotFoundException: referenceLibrary.json (Permission denied)` when running on the localfs backend. The reference-library workflow invoked `repseqio inferPoints` and `repseqio compile` with the same path for input and output (`referenceLibrary.json`). On localfs, input files are mounted read-only, so the tool could read them but the final write back failed. The output is now written to a separate file (`referenceLibrary.out.json`).
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+
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+ ## 1.21.8
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+
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+ ### Patch Changes
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+
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+ - 2ac36c0: Bump mixr version to 4.7.0-347-develop (switch back to default GC)
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+
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  ## 1.21.7
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  ### Patch Changes
package/dist/tengo/tpl/export-report.plj.gz CHANGED
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package/dist/tengo/tpl/main.plj.gz CHANGED
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package/dist/tengo/tpl/mixcr-analyze.plj.gz CHANGED
Binary file
package/dist/tengo/tpl/mixcr-export.plj.gz CHANGED
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package/dist/tengo/tpl/prerun.plj.gz CHANGED
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package/dist/tengo/tpl/process.plj.gz CHANGED
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package/package.json CHANGED
@@ -1,11 +1,11 @@
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  {
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  "name": "@platforma-open/milaboratories.mixcr-amplicon-alignment.workflow",
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- "version": "1.21.7",
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+ "version": "1.21.9",
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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": "5.11.0",
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- "@platforma-open/milaboratories.software-mixcr": "4.7.0-343-develop",
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+ "@platforma-open/milaboratories.software-mixcr": "4.7.0-347-develop",
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  "@platforma-open/milaboratories.software-repseqio": "^2.5.0-13-master"
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  },
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  "devDependencies": {
package/src/repseqio-library.tpl.tengo CHANGED
@@ -74,13 +74,13 @@ self.body(func(inputs) {
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  arg("--force").
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  addFile("referenceLibrary.json", referenceLibrary).
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  arg("referenceLibrary.json").
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- arg("referenceLibrary.json").
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- saveFile("referenceLibrary.json").
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+ arg("referenceLibrary.out.json").
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+ saveFile("referenceLibrary.out.json").
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  addFile("vGene.fasta", vGeneFasta).
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  cpu(1).mem("4GB")
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  repseqioInferPointsVResult := repseqioInferPointsVCmd.run()
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- referenceLibraryV := repseqioInferPointsVResult.getFile("referenceLibrary.json")
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+ referenceLibraryV := repseqioInferPointsVResult.getFile("referenceLibrary.out.json")
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  repseqioInferPointsJCmd := exec.builder().
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  software(repseqioSw).
@@ -90,13 +90,13 @@ self.body(func(inputs) {
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  arg("--force").
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  addFile("referenceLibrary.json", referenceLibraryV).
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  arg("referenceLibrary.json").
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- arg("referenceLibrary.json").
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- saveFile("referenceLibrary.json").
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+ arg("referenceLibrary.out.json").
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+ saveFile("referenceLibrary.out.json").
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  addFile("jGene.fasta", jGeneFasta).
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  cpu(1).mem("4GB")
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  repseqioInferPointsJResult := repseqioInferPointsJCmd.run()
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- referenceLibraryJ := repseqioInferPointsJResult.getFile("referenceLibrary.json")
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+ referenceLibraryJ := repseqioInferPointsJResult.getFile("referenceLibrary.out.json")
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  repseqioCompileCmd := exec.builder().
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  software(repseqioSw).
@@ -104,14 +104,14 @@ self.body(func(inputs) {
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  arg("--force").
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  addFile("referenceLibrary.json", referenceLibraryJ).
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  arg("referenceLibrary.json").
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- arg("referenceLibrary.json").
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- saveFile("referenceLibrary.json").
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+ arg("referenceLibrary.out.json").
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+ saveFile("referenceLibrary.out.json").
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  addFile("vGene.fasta", vGeneFasta).
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  addFile("jGene.fasta", jGeneFasta).
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  cpu(1).mem("4GB")
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  repseqioCompileResult := repseqioCompileCmd.run()
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- referenceLibraryCompiled := repseqioCompileResult.getFile("referenceLibrary.json")
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+ referenceLibraryCompiled := repseqioCompileResult.getFile("referenceLibrary.out.json")
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  repseqioDebugCmd := exec.builder().
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  software(repseqioSw).