@platforma-open/milaboratories.mixcr-clonotyping-2.workflow 2.6.0 → 2.8.0
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/.turbo/turbo-test.log +10 -10
- package/CHANGELOG.md +18 -0
- package/dist/tengo/lib/calculate-export-specs.lib.tengo +4 -1
- package/dist/tengo/tpl/aggregate-by-clonotype-key.plj.gz +0 -0
- package/dist/tengo/tpl/calculate-preset-info.plj.gz +0 -0
- package/dist/tengo/tpl/list-presets.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-single-cell.plj.gz +0 -0
- package/dist/tengo/tpl/process.plj.gz +0 -0
- package/dist/tengo/tpl/test.columns-calculate.plj.gz +0 -0
- package/dist/tengo/tpl/test.columns.test.plj.gz +0 -0
- package/package.json +4 -4
- package/src/calculate-export-specs.lib.tengo +4 -1
- package/src/mixcr-export.tpl.tengo +10 -0
- package/src/process.tpl.tengo +4 -2
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-clonotyping-2/mixcr-clonotyping-2/.npmrc". Failed to replace env in config: ${NPMJS_TOKEN}
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> @platforma-open/milaboratories.mixcr-clonotyping-2.workflow@2.
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> @platforma-open/milaboratories.mixcr-clonotyping-2.workflow@2.8.0 build /home/runner/work/mixcr-clonotyping-2/mixcr-clonotyping-2/workflow
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> rm -rf dist && pl-tengo check && pl-tengo build
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info: Skipping unknown file type: test/columns.test.ts
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package/.turbo/turbo-test.log
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WARN Issue while reading "/home/runner/work/mixcr-clonotyping-2/mixcr-clonotyping-2/.npmrc". Failed to replace env in config: ${NPMJS_TOKEN}
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> @platforma-open/milaboratories.mixcr-clonotyping-2.workflow@2.
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> @platforma-open/milaboratories.mixcr-clonotyping-2.workflow@2.8.0 test /home/runner/work/mixcr-clonotyping-2/mixcr-clonotyping-2/workflow
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> vitest
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[1m[7m[36m RUN [39m[27m[22m [36mv2.1.8 [39m[90m/home/runner/work/mixcr-clonotyping-2/mixcr-clonotyping-2/workflow[39m
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[32m✓[39m src/test/columns.test.ts [2m([22m[2m6 tests[22m[2m)[22m[33m
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[33m[2m✓[22m[39m checking preset for 'milab-human-dna-xcr-7genes-multiplex' [
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[33m[2m✓[22m[39m checking preset for '10x-sc-xcr-vdj' [
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[33m[2m✓[22m[39m checking preset for 'cellecta-human-rna-xcr-umi-drivermap-…' [
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[33m[2m✓[22m[39m checking preset for 'takara-human-rna-bcr-umi-smartseq' [
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[33m[2m✓[22m[39m checking preset for 'rna-seq' [
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[33m[2m✓[22m[39m checking preset for 'generic-single-cell-gex' [
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[32m✓[39m src/test/columns.test.ts [2m([22m[2m6 tests[22m[2m)[22m[33m 54112[2mms[22m[39m
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[33m[2m✓[22m[39m checking preset for 'milab-human-dna-xcr-7genes-multiplex' [33m12976[2mms[22m[39m
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[33m[2m✓[22m[39m checking preset for '10x-sc-xcr-vdj' [33m8593[2mms[22m[39m
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[33m[2m✓[22m[39m checking preset for 'cellecta-human-rna-xcr-umi-drivermap-…' [33m8350[2mms[22m[39m
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[33m[2m✓[22m[39m checking preset for 'takara-human-rna-bcr-umi-smartseq' [33m8290[2mms[22m[39m
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[33m[2m✓[22m[39m checking preset for 'rna-seq' [33m7833[2mms[22m[39m
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[33m[2m✓[22m[39m checking preset for 'generic-single-cell-gex' [33m8069[2mms[22m[39m
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[2m Test Files [22m [1m[32m1 passed[39m[22m[90m (1)[39m
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[2m Tests [22m [1m[32m6 passed[39m[22m[90m (6)[39m
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[2m Start at [22m
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[2m Duration [22m
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[2m Start at [22m 15:43:44
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[2m Duration [22m 55.17s[2m (transform 63ms, setup 0ms, collect 737ms, tests 54.11s, environment 0ms, prepare 92ms)[22m
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package/CHANGELOG.md
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# @platforma-open/milaboratories.mixcr-clonotyping.workflow
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## 2.8.0
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### Minor Changes
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- 22a4bd4: passing library into exportClones template
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## 2.7.0
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### Minor Changes
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- a3d8933: ampliseq preset bug correction
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## 2.6.1
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### Patch Changes
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- 24b689b: Fixes spec for mutation columns (adds pl7.app/vdj/gene domain to make column ids for V and J genes distinguishable)
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## 2.6.0
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### Minor Changes
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@@ -46,7 +46,7 @@ assemblingFeatureInfo := func(assemblingFeature) {
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splittedFeature := text.split(assemblingFeature, "_TO_")
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if len(splittedFeature) == 2 {
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if splittedFeature[1] == "FR4" {
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productiveFeature =
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productiveFeature = splittedFeature[0] + "_TO_FR4(0,-1)"
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coreVFeature = "{"+splittedFeature[0]+"Begin:FR3End}"
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coreJFeature = "FR4"
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} else {
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@@ -417,6 +417,9 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
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spec: {
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valueType: variant.valueType,
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name: "pl7.app/vdj/sequence/" + alphabetShortMixcr + variant.name,
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domain: {
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"pl7.app/vdj/gene": geneU
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},
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annotations: a(orderP, false, {
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"pl7.app/label": alphabetShort + variant.labelPart + geneU + " gene"
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})
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package/package.json
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{
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"name": "@platforma-open/milaboratories.mixcr-clonotyping-2.workflow",
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"version": "2.
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"version": "2.8.0",
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"description": "Tengo-based template",
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"dependencies": {
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"@platforma-sdk/workflow-tengo": "^
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"@platforma-sdk/workflow-tengo": "^4.0.3",
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"@platforma-open/milaboratories.mixcr-clonotyping-2.single-cell-scripts": "1.1.1"
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},
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"devDependencies": {
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"@platforma-sdk/tengo-builder": "^2.0.
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"@platforma-sdk/tengo-builder": "^2.0.3",
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"@platforma-open/milaboratories.software-mixcr": "4.7.0-149-develop",
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"@platforma-open/milaboratories.software-ptransform": "^1.3.1",
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"@platforma-sdk/test": "^1.
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"@platforma-sdk/test": "^1.28.2",
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"vitest": "^2.1.8",
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"typescript": "~5.5.4"
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},
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splittedFeature := text.split(assemblingFeature, "_TO_")
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if len(splittedFeature) == 2 {
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if splittedFeature[1] == "FR4" {
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productiveFeature =
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productiveFeature = splittedFeature[0] + "_TO_FR4(0,-1)"
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coreVFeature = "{"+splittedFeature[0]+"Begin:FR3End}"
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coreJFeature = "FR4"
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} else {
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spec: {
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valueType: variant.valueType,
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name: "pl7.app/vdj/sequence/" + alphabetShortMixcr + variant.name,
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domain: {
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"pl7.app/vdj/gene": geneU
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},
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annotations: a(orderP, false, {
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"pl7.app/label": alphabetShort + variant.labelPart + geneU + " gene"
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})
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clnsFile := inputs[pConstants.VALUE_FIELD_NAME]
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params := inputs.params
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library := inputs.library
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isLibraryFileGzipped := params.isLibraryFileGzipped
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chains := params.chains
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exportArgs := params.exportArgs
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arg("--reset-export-clone-table-splitting").
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arg("--chains").arg(chains)
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if library {
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if isLibraryFileGzipped {
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mixcrCmdBuilder.addFile("library.json.gz", library)
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} else {
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mixcrCmdBuilder.addFile("library.json", library)
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}
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}
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additionalAction(mixcrCmdBuilder)
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return mixcrCmdBuilder.
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package/src/process.tpl.tengo
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clonotypeKeyColumns: clonotypeKeyColumns,
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clonotypeKeyArgs: clonotypeKeyArgs,
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cellTagColumns: cellTagColumns,
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exportArgs: exportArgs
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exportArgs: exportArgs,
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isLibraryFileGzipped: isLibraryFileGzipped
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},
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library: library
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}
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}
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)
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