Merge pull request #1758 from milaboratory/mitool-tag-types

mitool tags types
milaboratory · Sep 5, 2024 · e555e82 · e555e82
2 parents 9e32b40 + 7b3654d
commit e555e82
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Showing 58 changed files with 2,099 additions and 409 deletions.
diff --git a/build.gradle.kts b/build.gradle.kts
@@ -134,13 +134,13 @@ val toObfuscate: Configuration by configurations.creating {
 val obfuscationLibs: Configuration by configurations.creating
 
 
-val mixcrAlgoVersion = "4.7.0-2-fix-freeze"
+val mixcrAlgoVersion = "4.7.0-18-mitool-tag-types"
 // may be blank (will be inherited from mixcr-algo)
-val milibVersion = "3.5.0-1-add-progress-to-fasta"
+val milibVersion = ""
 // may be blank (will be inherited from mixcr-algo or milib)
 val miuVersion = ""
 // may be blank (will be inherited from mixcr-algo)
-val mitoolVersion = ""
+val mitoolVersion = "2.3.0-17-mitool-tag-types"
 // may be blank (will be inherited from mixcr-algo)
 val repseqioVersion = ""
 

diff --git a/changelogs/v4.7.1.md b/changelogs/v4.7.1.md
@@ -1,3 +1,8 @@
 ## 🛠️ Other improvements & fixes
 
 - Tracking the progres of fasta[.gz] inputs on `align`.
+
+
+## 📚 New Presets
+
+- Added preset `bruker-human-sc-xcr-vdj-beacon` for TCR/BCR analyses of Bruker Beacon data  
diff --git a/regression/presets/analyze/10x-sc-xcr-vdj.yaml b/regression/presets/analyze/10x-sc-xcr-vdj.yaml
@@ -20,10 +20,11 @@ mitool:
     trimmingQualityThreshold: null
     trimmingWindowSize: null
     replaceWildcards: true
+    splitBySample: true
   refineTags:
-    tags:
-      - CELL
-      - UMI
+    tagTypes:
+      - Cell
+      - Molecule
     whitelists:
       CELL: builtin:737K-august-2016
     parameters:
@@ -65,11 +66,11 @@ mitool:
         minRecordWeightForUse: 0
         maxIterationsPerConsensus: 8
         maxConsensuses: 0
-      groupingTags:
-        - CELL
-        - UMI
-      payloadTags:
-        - R2
+      groupingTagTypes:
+        - Cell
+        - Molecule
+      payloadTagTypes:
+        - Targets
       safeUnusedReads: true
       safeDiscardedReads: true
       inferMinRecordsPerConsensus: true
@@ -102,11 +103,11 @@ mitool:
         minRecordWeightForUse: 0
         maxIterationsPerConsensus: 8
         maxConsensuses: 0
-      groupingTags:
-        - CELL
-        - UMI
-      payloadTags:
-        - R2
+      groupingTagTypes:
+        - Cell
+        - Molecule
+      payloadTagTypes:
+        - Targets
       safeUnusedReads: true
       safeDiscardedReads: true
       inferMinRecordsPerConsensus: true
@@ -139,10 +140,10 @@ mitool:
         minRecordWeightForUse: 0
         maxIterationsPerConsensus: 8
         maxConsensuses: 0
-      groupingTags:
-        - CELL
-      payloadTags:
-        - R2
+      groupingTagTypes:
+        - Cell
+      payloadTagTypes:
+        - Targets
       safeUnusedReads: true
       safeDiscardedReads: true
       inferMinRecordsPerConsensus: true
@@ -175,10 +176,10 @@ mitool:
         minRecordWeightForUse: 2
         maxIterationsPerConsensus: 8
         maxConsensuses: 0
-      groupingTags:
-        - CELL
-      payloadTags:
-        - R2
+      groupingTagTypes:
+        - Cell
+      payloadTagTypes:
+        - Targets
       safeUnusedReads: true
       safeDiscardedReads: true
       inferMinRecordsPerConsensus: true

diff --git a/regression/presets/analyze/10x-vdj-bcr-full-length.yaml b/regression/presets/analyze/10x-vdj-bcr-full-length.yaml
@@ -20,10 +20,11 @@ mitool:
     trimmingQualityThreshold: null
     trimmingWindowSize: null
     replaceWildcards: true
+    splitBySample: true
   refineTags:
-    tags:
-      - CELL
-      - UMI
+    tagTypes:
+      - Cell
+      - Molecule
     whitelists:
       CELL: builtin:737K-august-2016
     parameters:
@@ -65,11 +66,11 @@ mitool:
         minRecordWeightForUse: 0
         maxIterationsPerConsensus: 8
         maxConsensuses: 0
-      groupingTags:
-        - CELL
-        - UMI
-      payloadTags:
-        - R2
+      groupingTagTypes:
+        - Cell
+        - Molecule
+      payloadTagTypes:
+        - Targets
       safeUnusedReads: true
       safeDiscardedReads: true
       inferMinRecordsPerConsensus: true
@@ -102,11 +103,11 @@ mitool:
         minRecordWeightForUse: 0
         maxIterationsPerConsensus: 8
         maxConsensuses: 0
-      groupingTags:
-        - CELL
-        - UMI
-      payloadTags:
-        - R2
+      groupingTagTypes:
+        - Cell
+        - Molecule
+      payloadTagTypes:
+        - Targets
       safeUnusedReads: true
       safeDiscardedReads: true
       inferMinRecordsPerConsensus: true
@@ -139,10 +140,10 @@ mitool:
         minRecordWeightForUse: 0
         maxIterationsPerConsensus: 8
         maxConsensuses: 0
-      groupingTags:
-        - CELL
-      payloadTags:
-        - R2
+      groupingTagTypes:
+        - Cell
+      payloadTagTypes:
+        - Targets
       safeUnusedReads: true
       safeDiscardedReads: true
       inferMinRecordsPerConsensus: true
@@ -175,10 +176,10 @@ mitool:
         minRecordWeightForUse: 2
         maxIterationsPerConsensus: 8
         maxConsensuses: 0
-      groupingTags:
-        - CELL
-      payloadTags:
-        - R2
+      groupingTagTypes:
+        - Cell
+      payloadTagTypes:
+        - Targets
       safeUnusedReads: true
       safeDiscardedReads: true
       inferMinRecordsPerConsensus: true

diff --git a/regression/presets/analyze/10x-vdj-bcr.yaml b/regression/presets/analyze/10x-vdj-bcr.yaml
@@ -20,10 +20,11 @@ mitool:
     trimmingQualityThreshold: null
     trimmingWindowSize: null
     replaceWildcards: true
+    splitBySample: true
   refineTags:
-    tags:
-      - CELL
-      - UMI
+    tagTypes:
+      - Cell
+      - Molecule
     whitelists:
       CELL: builtin:737K-august-2016
     parameters:
@@ -65,11 +66,11 @@ mitool:
         minRecordWeightForUse: 0
         maxIterationsPerConsensus: 8
         maxConsensuses: 0
-      groupingTags:
-        - CELL
-        - UMI
-      payloadTags:
-        - R2
+      groupingTagTypes:
+        - Cell
+        - Molecule
+      payloadTagTypes:
+        - Targets
       safeUnusedReads: true
       safeDiscardedReads: true
       inferMinRecordsPerConsensus: true
@@ -102,11 +103,11 @@ mitool:
         minRecordWeightForUse: 0
         maxIterationsPerConsensus: 8
         maxConsensuses: 0
-      groupingTags:
-        - CELL
-        - UMI
-      payloadTags:
-        - R2
+      groupingTagTypes:
+        - Cell
+        - Molecule
+      payloadTagTypes:
+        - Targets
       safeUnusedReads: true
       safeDiscardedReads: true
       inferMinRecordsPerConsensus: true
@@ -139,10 +140,10 @@ mitool:
         minRecordWeightForUse: 0
         maxIterationsPerConsensus: 8
         maxConsensuses: 0
-      groupingTags:
-        - CELL
-      payloadTags:
-        - R2
+      groupingTagTypes:
+        - Cell
+      payloadTagTypes:
+        - Targets
       safeUnusedReads: true
       safeDiscardedReads: true
       inferMinRecordsPerConsensus: true
@@ -175,10 +176,10 @@ mitool:
         minRecordWeightForUse: 2
         maxIterationsPerConsensus: 8
         maxConsensuses: 0
-      groupingTags:
-        - CELL
-      payloadTags:
-        - R2
+      groupingTagTypes:
+        - Cell
+      payloadTagTypes:
+        - Targets
       safeUnusedReads: true
       safeDiscardedReads: true
       inferMinRecordsPerConsensus: true

diff --git a/regression/presets/analyze/10x-vdj-tcr-alias-multi-barcode-test.yaml b/regression/presets/analyze/10x-vdj-tcr-alias-multi-barcode-test.yaml
@@ -20,10 +20,11 @@ mitool:
     trimmingQualityThreshold: null
     trimmingWindowSize: null
     replaceWildcards: true
+    splitBySample: true
   refineTags:
-    tags:
-      - CELL
-      - UMI
+    tagTypes:
+      - Cell
+      - Molecule
     whitelists:
       CELL: builtin:737K-august-2016
     parameters:
@@ -65,11 +66,11 @@ mitool:
         minRecordWeightForUse: 0
         maxIterationsPerConsensus: 8
         maxConsensuses: 0
-      groupingTags:
-        - CELL
-        - UMI
-      payloadTags:
-        - R2
+      groupingTagTypes:
+        - Cell
+        - Molecule
+      payloadTagTypes:
+        - Targets
       safeUnusedReads: true
       safeDiscardedReads: true
       inferMinRecordsPerConsensus: true
@@ -102,11 +103,11 @@ mitool:
         minRecordWeightForUse: 0
         maxIterationsPerConsensus: 8
         maxConsensuses: 0
-      groupingTags:
-        - CELL
-        - UMI
-      payloadTags:
-        - R2
+      groupingTagTypes:
+        - Cell
+        - Molecule
+      payloadTagTypes:
+        - Targets
       safeUnusedReads: true
       safeDiscardedReads: true
       inferMinRecordsPerConsensus: true
@@ -139,10 +140,10 @@ mitool:
         minRecordWeightForUse: 0
         maxIterationsPerConsensus: 8
         maxConsensuses: 0
-      groupingTags:
-        - CELL
-      payloadTags:
-        - R2
+      groupingTagTypes:
+        - Cell
+      payloadTagTypes:
+        - Targets
       safeUnusedReads: true
       safeDiscardedReads: true
       inferMinRecordsPerConsensus: true
@@ -175,10 +176,10 @@ mitool:
         minRecordWeightForUse: 2
         maxIterationsPerConsensus: 8
         maxConsensuses: 0
-      groupingTags:
-        - CELL
-      payloadTags:
-        - R2
+      groupingTagTypes:
+        - Cell
+      payloadTagTypes:
+        - Targets
       safeUnusedReads: true
       safeDiscardedReads: true
       inferMinRecordsPerConsensus: true