@platforma-open/milaboratories.mixcr-amplicon-alignment.workflow 1.21.8 → 1.21.9
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/.turbo/turbo-build.log +1 -1
- package/CHANGELOG.md +6 -0
- package/dist/tengo/tpl/aggregate-by-clonotype-key.plj.gz +0 -0
- package/dist/tengo/tpl/export-report.plj.gz +0 -0
- package/dist/tengo/tpl/main.plj.gz +0 -0
- package/dist/tengo/tpl/mixcr-analyze.plj.gz +0 -0
- package/dist/tengo/tpl/mixcr-export.plj.gz +0 -0
- package/dist/tengo/tpl/prerun.plj.gz +0 -0
- package/dist/tengo/tpl/process.plj.gz +0 -0
- package/dist/tengo/tpl/repseqio-library.plj.gz +0 -0
- package/package.json +1 -1
- package/src/repseqio-library.tpl.tengo +9 -9
package/.turbo/turbo-build.log
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@@ -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.
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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"...
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package/CHANGELOG.md
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# @platforma-open/milaboratories.mixcr-amplicon-alignment.workflow
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## 1.21.9
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### Patch Changes
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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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## 1.21.8
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### Patch Changes
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package/package.json
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@@ -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).
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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).
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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).
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