@platforma-open/milaboratories.mixcr-clonotyping-2.workflow 2.13.0 → 2.14.1

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Files changed (17) hide show
  1. package/.turbo/turbo-build.log +14 -14
  2. package/.turbo/turbo-test.log +27 -12
  3. package/CHANGELOG.md +12 -0
  4. package/dist/tengo/tpl/aggregate-by-clonotype-key.plj.gz +0 -0
  5. package/dist/tengo/tpl/calculate-preset-info.plj.gz +0 -0
  6. package/dist/tengo/tpl/list-presets.plj.gz +0 -0
  7. package/dist/tengo/tpl/main.plj.gz +0 -0
  8. package/dist/tengo/tpl/mixcr-analyze.plj.gz +0 -0
  9. package/dist/tengo/tpl/mixcr-export.plj.gz +0 -0
  10. package/dist/tengo/tpl/prerun.plj.gz +0 -0
  11. package/dist/tengo/tpl/process-single-cell.plj.gz +0 -0
  12. package/dist/tengo/tpl/process.plj.gz +0 -0
  13. package/dist/tengo/tpl/test.columns-calculate.plj.gz +0 -0
  14. package/dist/tengo/tpl/test.columns.test.plj.gz +0 -0
  15. package/package.json +2 -2
  16. package/src/mixcr-export.tpl.tengo +24 -1
  17. package/src/process.tpl.tengo +8 -1
package/.turbo/turbo-build.log CHANGED
@@ -1,6 +1,6 @@
1
-  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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+  WARN  Issue while reading "/home/runner/work/mixcr-clonotyping/mixcr-clonotyping/.npmrc". Failed to replace env in config: ${NPMJS_TOKEN}
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- > @platforma-open/milaboratories.mixcr-clonotyping-2.workflow@2.13.0 build /home/runner/work/mixcr-clonotyping-2/mixcr-clonotyping-2/workflow
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+ > @platforma-open/milaboratories.mixcr-clonotyping-2.workflow@2.14.1 build /home/runner/work/mixcr-clonotyping/mixcr-clonotyping/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
@@ -19,17 +19,17 @@ Processing "src/test/columns.test.tpl.tengo"...
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  No syntax errors found.
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  info: Skipping unknown file type: test/columns.test.ts
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  info: Compiling 'dist'...
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- info: - writing /home/runner/work/mixcr-clonotyping-2/mixcr-clonotyping-2/workflow/dist/tengo/lib/calculate-export-specs.lib.tengo
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- info: - writing /home/runner/work/mixcr-clonotyping-2/mixcr-clonotyping-2/workflow/dist/tengo/tpl/aggregate-by-clonotype-key.plj.gz
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- info: - writing /home/runner/work/mixcr-clonotyping-2/mixcr-clonotyping-2/workflow/dist/tengo/tpl/calculate-preset-info.plj.gz
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- info: - writing /home/runner/work/mixcr-clonotyping-2/mixcr-clonotyping-2/workflow/dist/tengo/tpl/list-presets.plj.gz
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- info: - writing /home/runner/work/mixcr-clonotyping-2/mixcr-clonotyping-2/workflow/dist/tengo/tpl/mixcr-analyze.plj.gz
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- info: - writing /home/runner/work/mixcr-clonotyping-2/mixcr-clonotyping-2/workflow/dist/tengo/tpl/mixcr-export.plj.gz
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- info: - writing /home/runner/work/mixcr-clonotyping-2/mixcr-clonotyping-2/workflow/dist/tengo/tpl/prerun.plj.gz
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- info: - writing /home/runner/work/mixcr-clonotyping-2/mixcr-clonotyping-2/workflow/dist/tengo/tpl/process-single-cell.plj.gz
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- info: - writing /home/runner/work/mixcr-clonotyping-2/mixcr-clonotyping-2/workflow/dist/tengo/tpl/process.plj.gz
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- info: - writing /home/runner/work/mixcr-clonotyping-2/mixcr-clonotyping-2/workflow/dist/tengo/tpl/test.columns-calculate.plj.gz
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- info: - writing /home/runner/work/mixcr-clonotyping-2/mixcr-clonotyping-2/workflow/dist/tengo/tpl/test.columns.test.plj.gz
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- info: - writing /home/runner/work/mixcr-clonotyping-2/mixcr-clonotyping-2/workflow/dist/tengo/tpl/main.plj.gz
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+ info: - writing /home/runner/work/mixcr-clonotyping/mixcr-clonotyping/workflow/dist/tengo/lib/calculate-export-specs.lib.tengo
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+ info: - writing /home/runner/work/mixcr-clonotyping/mixcr-clonotyping/workflow/dist/tengo/tpl/aggregate-by-clonotype-key.plj.gz
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+ info: - writing /home/runner/work/mixcr-clonotyping/mixcr-clonotyping/workflow/dist/tengo/tpl/calculate-preset-info.plj.gz
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+ info: - writing /home/runner/work/mixcr-clonotyping/mixcr-clonotyping/workflow/dist/tengo/tpl/list-presets.plj.gz
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+ info: - writing /home/runner/work/mixcr-clonotyping/mixcr-clonotyping/workflow/dist/tengo/tpl/mixcr-analyze.plj.gz
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+ info: - writing /home/runner/work/mixcr-clonotyping/mixcr-clonotyping/workflow/dist/tengo/tpl/mixcr-export.plj.gz
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+ info: - writing /home/runner/work/mixcr-clonotyping/mixcr-clonotyping/workflow/dist/tengo/tpl/prerun.plj.gz
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+ info: - writing /home/runner/work/mixcr-clonotyping/mixcr-clonotyping/workflow/dist/tengo/tpl/process-single-cell.plj.gz
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+ info: - writing /home/runner/work/mixcr-clonotyping/mixcr-clonotyping/workflow/dist/tengo/tpl/process.plj.gz
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+ info: - writing /home/runner/work/mixcr-clonotyping/mixcr-clonotyping/workflow/dist/tengo/tpl/test.columns-calculate.plj.gz
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+ info: - writing /home/runner/work/mixcr-clonotyping/mixcr-clonotyping/workflow/dist/tengo/tpl/test.columns.test.plj.gz
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+ info: - writing /home/runner/work/mixcr-clonotyping/mixcr-clonotyping/workflow/dist/tengo/tpl/main.plj.gz
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  info: Template Pack build done.
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  info: Template Pack build done.
package/.turbo/turbo-test.log CHANGED
@@ -1,21 +1,36 @@
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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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+  WARN  Issue while reading "/home/runner/work/mixcr-clonotyping/mixcr-clonotyping/.npmrc". Failed to replace env in config: ${NPMJS_TOKEN}
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- > @platforma-open/milaboratories.mixcr-clonotyping-2.workflow@2.13.0 test /home/runner/work/mixcr-clonotyping-2/mixcr-clonotyping-2/workflow
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+ > @platforma-open/milaboratories.mixcr-clonotyping-2.workflow@2.14.1 test /home/runner/work/mixcr-clonotyping/mixcr-clonotyping/workflow
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  > vitest
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-  RUN  v2.1.8 /home/runner/work/mixcr-clonotyping-2/mixcr-clonotyping-2/workflow
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+  RUN  v2.1.8 /home/runner/work/mixcr-clonotyping/mixcr-clonotyping/workflow
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- ✓ src/test/columns.test.ts (6 tests) 53338ms
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- ✓ checking preset for 'milab-human-dna-xcr-7genes-multiplex' 13323ms
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- ✓ checking preset for '10x-sc-xcr-vdj' 8239ms
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- ✓ checking preset for 'cellecta-human-rna-xcr-umi-drivermap-…' 8196ms
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- ✓ checking preset for 'takara-human-rna-bcr-umi-smartseq' 8030ms
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- ✓ checking preset for 'rna-seq' 7570ms
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- ✓ checking preset for 'generic-single-cell-gex' 7979ms
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+ stdout | src/test/columns.test.ts > checking preset for 'milab-human-dna-xcr-7genes-multiplex'
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+ {
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+ type: 'ok',
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+ value: undefined,
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+ stable: false,
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+ uTag: 'fc1997c6-5b87-4c86-8aa6-0ea9d2014b38',
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+ unstableMarker: 'field_not_resolved:exportSpecs'
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+ }
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+
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+ stdout | src/test/columns.test.ts > checking preset for 'milab-human-dna-xcr-7genes-multiplex'
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+ TEST FAILED SO ALTERNATIVE ROOT IS PRESETVED IN PL: test_1745591248072_67adc363-cf48-41ba-82a1-fe7e00142ad8 (NG:0x82)
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+
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+ stdout | src/test/columns.test.ts > checking preset for 'milab-human-dna-xcr-7genes-multiplex'
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+ TEST FAILED SO ALTERNATIVE ROOT IS PRESETVED IN PL: test_1745591269056_11ea8a8b-adb0-49ca-b74e-a9b287bc1ae3 (NG:0x138)
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+
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+ ✓ src/test/columns.test.ts (6 tests) 67551ms
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+ ✓ checking preset for 'milab-human-dna-xcr-7genes-multiplex' 27568ms
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+ ✓ checking preset for '10x-sc-xcr-vdj' 8418ms
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+ ✓ checking preset for 'cellecta-human-rna-xcr-umi-drivermap-…' 8182ms
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+ ✓ checking preset for 'takara-human-rna-bcr-umi-smartseq' 7939ms
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+ ✓ checking preset for 'rna-seq' 7749ms
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+ ✓ checking preset for 'generic-single-cell-gex' 7693ms
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   Test Files  1 passed (1)
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   Tests  6 passed (6)
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-  Start at  16:55:46
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-  Duration  54.14s (transform 43ms, setup 0ms, collect 576ms, tests 53.34s, environment 0ms, prepare 59ms)
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+  Start at  14:27:27
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+  Duration  68.34s (transform 42ms, setup 0ms, collect 576ms, tests 67.55s, environment 0ms, prepare 60ms)
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package/CHANGELOG.md CHANGED
@@ -1,5 +1,17 @@
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  # @platforma-open/milaboratories.mixcr-clonotyping.workflow
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+ ## 2.14.1
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+
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+ ### Patch Changes
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+
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+ - 748457a: Upgrade mixcr version to prevent crash with custom library with custom C gene names
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+
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+ ## 2.14.0
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+
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+ ### Minor Changes
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+
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+ - dc86a17: single cell export and removing columns for secondary clones except CDR3 aa
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+
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  ## 2.13.0
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  ### Minor Changes
package/dist/tengo/tpl/list-presets.plj.gz CHANGED
Binary file
package/dist/tengo/tpl/main.plj.gz CHANGED
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package/dist/tengo/tpl/mixcr-analyze.plj.gz CHANGED
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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
@@ -1,6 +1,6 @@
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  {
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  "name": "@platforma-open/milaboratories.mixcr-clonotyping-2.workflow",
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- "version": "2.13.0",
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+ "version": "2.14.1",
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  "description": "Tengo-based template",
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  "dependencies": {
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  "@platforma-sdk/workflow-tengo": "^4.1.2",
@@ -9,7 +9,7 @@
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  },
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  "devDependencies": {
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  "@platforma-sdk/tengo-builder": "^2.1.0",
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- "@platforma-open/milaboratories.software-mixcr": "4.7.0-164-develop",
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+ "@platforma-open/milaboratories.software-mixcr": "4.7.0-165-develop",
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  "@platforma-open/milaboratories.software-ptransform": "^1.3.1",
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  "@platforma-sdk/test": "^1.29.17",
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  "vitest": "~2.1.8",
package/src/mixcr-export.tpl.tengo CHANGED
@@ -75,7 +75,8 @@ self.body(func(inputs) {
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  if is_undefined(clonotypeKeyColumns) {
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  result.tsv = unprocessedTsv
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- } else {
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+
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+ } else if is_undefined(cellTagColumns) {
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  hashCmdBuilder := exec.builder().
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  printErrStreamToStdout().
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  software(hashColumnSw).
@@ -96,6 +97,28 @@ self.body(func(inputs) {
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  processedTsv := hashCmd.getFile("output.tsv")
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+ result.tsv = processedTsv
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+
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+ } else {
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+ pWorkflow := {
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+ steps: [ {
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+ type: "combine_columns_as_json",
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+ src: clonotypeKeyColumns,
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+ dst: "clonotypeKey"
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+ } ]
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+ }
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+
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+ aggregateCmd := exec.builder().
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+ printErrStreamToStdout().
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+ software(ptransformSw).
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+ arg("--workflow").arg("wf.json").
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+ writeFile("wf.json", json.encode(pWorkflow)).
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+ arg("input.tsv").addFile("input.tsv", unprocessedTsv).
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+ arg("output.tsv").saveFile("output.tsv").
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+ run()
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+
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+ processedTsv := aggregateCmd.getFile("output.tsv")
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+
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  result.tsv = processedTsv
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  }
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package/src/process.tpl.tengo CHANGED
@@ -472,6 +472,13 @@ self.body(func(inputs) {
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  path: ["clonotypeTsv"]
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  } ]
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+ //removing columns from secondary chain except aaSeqCDR3
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+ columnsSpecPerClonotypeSecondary := []
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+ for col in columnsSpecPerClonotype {
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+ if col.column == "aaSeqCDR3" {
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+ columnsSpecPerClonotypeSecondary += [ col ]
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+ }
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+ }
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  for chainIdx in [0, 1] {
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  // "A" chain is always the one that is more diverse
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  chainLetterU := ["A", "B"][chainIdx]
@@ -517,7 +524,7 @@ self.body(func(inputs) {
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  xsvType: "tsv",
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  settings: {
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  axes: axesByScClonotypeKeyWithReceptor,
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- columns: transformSpecs(columnsSpecPerClonotype, {
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+ columns: transformSpecs(isPrimary ? columnsSpecPerClonotype : columnsSpecPerClonotypeSecondary, {
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  spec: {
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  domain: {
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  "pl7.app/vdj/scClonotypeChain": chainLetterU,