@platforma-open/milaboratories.rarefaction.workflow 1.1.7 → 1.1.9
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
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@@ -1,6 +1,6 @@
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WARN Issue while reading "/home/runner/work/rarefaction/rarefaction/.npmrc". Failed to replace env in config: ${NPMJS_TOKEN}
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> @platforma-open/milaboratories.rarefaction.workflow@1.1.
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> @platforma-open/milaboratories.rarefaction.workflow@1.1.9 build /home/runner/work/rarefaction/rarefaction/workflow
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> rm -rf dist && pl-tengo check && pl-tengo build
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Processing "src/main.tpl.tengo"...
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package/CHANGELOG.md
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@@ -1,5 +1,20 @@
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# @platforma-open/milaboratories.rarefaction.workflow
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## 1.1.9
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### Patch Changes
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- 0075c7e: Propagate user memory setting to TSV builder to prevent OOM on large datasets
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- 1573d0e: Update SDK dependencies to latest versions
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## 1.1.8
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### Patch Changes
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- 770f778: Show warning when selected dataset contains no clonotypes
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- Updated dependencies [770f778]
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- @platforma-open/milaboratories.rarefaction.software@1.2.6
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## 1.1.7
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### Patch Changes
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Binary file
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Binary file
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package/package.json
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@@ -1,14 +1,14 @@
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{
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"name": "@platforma-open/milaboratories.rarefaction.workflow",
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"version": "1.1.
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"version": "1.1.9",
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"type": "module",
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"description": "Tengo-based template",
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"dependencies": {
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"@platforma-sdk/workflow-tengo": "5.
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"@platforma-open/milaboratories.rarefaction.software": "1.2.
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"@platforma-sdk/workflow-tengo": "5.11.0",
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"@platforma-open/milaboratories.rarefaction.software": "1.2.6"
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},
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"devDependencies": {
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"@platforma-sdk/tengo-builder": "2.
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"@platforma-sdk/tengo-builder": "2.5.5"
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},
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"scripts": {
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"build": "rm -rf dist && pl-tengo check && pl-tengo build",
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package/src/main.tpl.tengo
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@@ -100,7 +100,11 @@ wf.prepare(func(args) {
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wf.body(func(args) {
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datasetSpec := args.columns.getSpec(args.datasetRef)
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convMem := string(args.mem) + "GiB"
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tsvBuilder := pframes.tsvFileBuilder()
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tsvBuilder.mem(convMem)
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tsvBuilder.cpu(1)
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tsvBuilder.add(args.columns.getColumn("abundance"), {header: "abundance"})
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tsvBuilder.setAxisHeader(datasetSpec.axesSpec[1].name, "clonotypeKey")
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tsv := tsvBuilder.build()
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@@ -140,7 +144,8 @@ wf.body(func(args) {
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return {
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outputs: {
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rarefactionPFrame: pframes.exportFrame(tracedPFrame),
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rarefactionLogs: rarefactionRender.output("rarefactionLogs")
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rarefactionLogs: rarefactionRender.output("rarefactionLogs"),
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noData: rarefactionRender.output("noData")
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},
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exports: {}
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}
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@@ -17,7 +17,7 @@ self.validateInputs({
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}
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})
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self.defineOutputs(["rarefactionOutput", "rarefactionLogs"])
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self.defineOutputs(["rarefactionOutput", "rarefactionLogs", "noData"])
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self.body(func(args) {
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// Get input parameters
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arg(numIterations).
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arg(string(extrapolation)).
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saveFile(outfile).
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saveFileContent("noData.txt").
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saveStdoutStream().
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cacheMinutes(4*60).
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printErrStreamToStdout().
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return {
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rarefactionOutput: rarefactionCmd.getFile(outfile),
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rarefactionLogs: rarefactionCmd.getStdoutStream()
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rarefactionLogs: rarefactionCmd.getStdoutStream(),
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noData: rarefactionCmd.getFileContent("noData.txt")
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}
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})
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