Merge branch 'develop' into bruker_v2

* develop: (36 commits)
  regression tests automated change
  fix order
  regression tests automated change
  changelog
  --alleles-search-could-be-skipped
  regression tests automated change
  update version
  fix alignments diff
  fix: pl-pkg now uses 85% of ram in container
  fix sortBySequence with composite feature
  rename safe->save
  chore: fix pl-pkg name (#1827)
  Fix typo in package name
  Release to public npm (#1820)
  regression tests automated change
  changed bruker preset to species agnostic, added cell id barcode transformation
  regression tests automated change
  Fixed Layout for presets
  regression tests automated change
  regression tests automated change
  ...

.github/workflows/build.yaml

@@ -89,9 +89,17 @@ jobs:
       # Send notifications
       notify-telegram: true
 
+      # NPM publish
+      node-registry-url: 'https://registry.npmjs.org'
+      node-scope: '@platforma-open'
+      publish-to-public: true
+
     secrets:
       env: |
-        { "MI_LICENSE": ${{ toJSON(secrets.MI_LICENSE) }} }
+        {
+          "MI_LICENSE": ${{ toJSON(secrets.MI_LICENSE) }},
+          "NPMJS_TOKEN": ${{ toJSON(secrets.NPMJS_TOKEN) }}
+        }
 
       GRADLE_PROPERTIES: |
         org.gradle.caching=true

build.gradle.kts

@@ -134,7 +134,7 @@ val toObfuscate: Configuration by configurations.creating {
 val obfuscationLibs: Configuration by configurations.creating
 
 
-val mixcrAlgoVersion = "4.7.0-20-export-for-platforma"
+val mixcrAlgoVersion = "4.7.0-31-fixes"
 // may be blank (will be inherited from mixcr-algo)
 val milibVersion = ""
 // may be blank (will be inherited from mixcr-algo or milib)

changelogs/v4.7.1.md

@@ -1,8 +1,13 @@
 ## 🛠️ Other improvements & fixes
 
 - Tracking the progres of fasta[.gz] inputs on `align`.
-
+- Improved alignment rate of short parts of genes in reads with height rate of mutations
+- Fixed combination of `-Massemble.sortBySequence=true` and `--assemble-clonotypes-by` with composite feature
+- For `findShmTree` command `--alleles-search-could-be-skipped` option is added for special cases
 
 ## 📚 New Presets
 
-- Added preset `bruker-human-sc-xcr-vdj-beacon` for TCR/BCR analyses of Bruker Beacon data  
+- Added preset `bruker-human-sc-xcr-vdj-beacon` for TCR/BCR analyses of Bruker Beacon data  
+- Added presets for new Qiagen kits: `qiagen-human-rna-tcr-umi-targeted-qiaseq` and `qiagen-mouse-rna-tcr-umi-targeted-qiaseq`
+- Added preset `illumina-human-dna-trb-ampliseq-sr`
+- Removed layout for Illumina kits, iRepertoire and Thermofisher kits.

itests/case008.sh

@@ -29,10 +29,10 @@ mixcr analyze --verbose generic-amplicon \
   -Malign.parameters.readsLayout=Collinear \
   CD4M1_test_R1.fastq.gz CD4M1_test_R2.fastq.gz case8
 
-assert "cat case8.align.report.json | head -n 1 | jq -r .chainUsage.chains.TRA.total" "241313"
-assert "cat case8.assemble.report.json | head -n 1 | jq -r .readsInClones" "200731"
-assert "cat case8.assemble.report.json | head -n 1 | jq -r .clones" "25653"
+assert "cat case8.align.report.json | head -n 1 | jq -r .chainUsage.chains.TRA.total" "241364"
+assert "cat case8.assemble.report.json | head -n 1 | jq -r .readsInClones" "200784"
+assert "cat case8.assemble.report.json | head -n 1 | jq -r .clones" "25662"
 assert "cat case8.assembleContigs.report.json | head -n 1 | jq -r .longestContigLength" "499"
-assert "cat case8.assembleContigs.report.json | head -n 1 | jq -r .clonesWithAmbiguousLetters" "3543"
+assert "cat case8.assembleContigs.report.json | head -n 1 | jq -r .clonesWithAmbiguousLetters" "3547"
 assert "cat case8.assembleContigs.report.json | head -n 1 | jq -r .assemblePrematureTerminationEvents" "4"
-assert "cat case8.assembleContigs.report.json | head -n 1 | jq -r .finalCloneCount" "25653"
+assert "cat case8.assembleContigs.report.json | head -n 1 | jq -r .finalCloneCount" "25662"

itests/case009.sh

@@ -30,9 +30,9 @@ mixcr analyze --verbose generic-amplicon \
   -M align.parameters.readsLayout=Collinear \
   CD4M1_test_R1.fastq.gz CD4M1_test_R2.fastq.gz case9
 
-assert "cat case9.align.report.json | head -n 1 | jq -r .chainUsage.chains.TRA.total" "241313"
-assert "cat case9.assemble.report.json | head -n 1 | jq -r .readsInClones" "200731"
+assert "cat case9.align.report.json | head -n 1 | jq -r .chainUsage.chains.TRA.total" "241364"
+assert "cat case9.assemble.report.json | head -n 1 | jq -r .readsInClones" "200784"
 assert "cat case9.assembleContigs.report.json | head -n 1 | jq -r .longestContigLength" "499"
-assert "cat case9.assembleContigs.report.json | head -n 1 | jq -r .clonesWithAmbiguousLetters" "3543"
+assert "cat case9.assembleContigs.report.json | head -n 1 | jq -r .clonesWithAmbiguousLetters" "3547"
 assert "cat case9.assembleContigs.report.json | head -n 1 | jq -r .assemblePrematureTerminationEvents" "4"
-assert "cat case9.assembleContigs.report.json | head -n 1 | jq -r .finalCloneCount" "25653"
+assert "cat case9.assembleContigs.report.json | head -n 1 | jq -r .finalCloneCount" "25662"