Merge pull request #1452 from milaboratory/mixcr-regression-tests/Cel…

…l-grouping-finalizing Regression tests changes in the Cell-grouping-finalizing
milaboratory · Nov 30, 2023 · de4059e · de4059e
2 parents f22813f + ce39fdd
commit de4059e
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Showing 49 changed files with 498 additions and 453 deletions.
diff --git a/regression/presets/analyze/10x-5gex-cdr3.yaml b/regression/presets/analyze/10x-5gex-cdr3.yaml
@@ -400,23 +400,24 @@ exportCloneGroups:
     - field: -uniqueTagCount
       args:
         - Molecule
-    - field: -targetSequences
-    - field: -targetQualities
     - field: -vHitsWithScore
     - field: -dHitsWithScore
     - field: -jHitsWithScore
     - field: -cHitsWithScore
-    - field: -vAlignments
-    - field: -dAlignments
-    - field: -jAlignments
-    - field: -cAlignments
-    - field: -allNFeaturesWithMinQuality
-    - field: -allAAFeatures
-    - field: -defaultAnchorPoints
+    - field: -nFeature
+      args:
+        - CDR3
+    - field: -aaFeature
+      args:
+        - CDR3
   sortChainsBy: Auto
 qc:
   checks:
     - type: AlignmentsDroppedLowQuality
       upper: 0.2
       middle: 0.1
       label: Alignments dropped due to low sequence quality
+    - type: CellBarcodesWithFoundGroups
+      upper: 0.9
+      middle: 0.8
+      label: Cell barcodes used in result groups
diff --git a/regression/presets/analyze/10x-5gex-full-length.yaml b/regression/presets/analyze/10x-5gex-full-length.yaml
@@ -404,23 +404,24 @@ exportCloneGroups:
     - field: -uniqueTagCount
       args:
         - Molecule
-    - field: -targetSequences
-    - field: -targetQualities
     - field: -vHitsWithScore
     - field: -dHitsWithScore
     - field: -jHitsWithScore
     - field: -cHitsWithScore
-    - field: -vAlignments
-    - field: -dAlignments
-    - field: -jAlignments
-    - field: -cAlignments
-    - field: -allNFeaturesWithMinQuality
-    - field: -allAAFeatures
-    - field: -defaultAnchorPoints
+    - field: -nFeature
+      args:
+        - CDR3
+    - field: -aaFeature
+      args:
+        - CDR3
   sortChainsBy: Auto
 qc:
   checks:
     - type: AlignmentsDroppedLowQuality
       upper: 0.2
       middle: 0.1
       label: Alignments dropped due to low sequence quality
+    - type: CellBarcodesWithFoundGroups
+      upper: 0.9
+      middle: 0.8
+      label: Cell barcodes used in result groups
diff --git a/regression/presets/analyze/10x-sc-5gex.yaml b/regression/presets/analyze/10x-sc-5gex.yaml
@@ -400,23 +400,24 @@ exportCloneGroups:
     - field: -uniqueTagCount
       args:
         - Molecule
-    - field: -targetSequences
-    - field: -targetQualities
     - field: -vHitsWithScore
     - field: -dHitsWithScore
     - field: -jHitsWithScore
     - field: -cHitsWithScore
-    - field: -vAlignments
-    - field: -dAlignments
-    - field: -jAlignments
-    - field: -cAlignments
-    - field: -allNFeaturesWithMinQuality
-    - field: -allAAFeatures
-    - field: -defaultAnchorPoints
+    - field: -nFeature
+      args:
+        - CDR3
+    - field: -aaFeature
+      args:
+        - CDR3
   sortChainsBy: Auto
 qc:
   checks:
     - type: AlignmentsDroppedLowQuality
       upper: 0.2
       middle: 0.1
       label: Alignments dropped due to low sequence quality
+    - type: CellBarcodesWithFoundGroups
+      upper: 0.9
+      middle: 0.8
+      label: Cell barcodes used in result groups
diff --git a/regression/presets/analyze/10x-sc-xcr-vdj.yaml b/regression/presets/analyze/10x-sc-xcr-vdj.yaml
@@ -400,7 +400,7 @@ assemble:
                     - allTags:Molecule
               operator:
                 type: group_operator_cumtop
-                share: 0.95
+                share: 0.8
                 accept: High
               expectedSorting:
                 - allTags:Molecule
@@ -429,7 +429,7 @@ assemble:
                   reportHist: null
               operator:
                 type: group_operator_cumtop
-                share: 0.95
+                share: 0.9
                 accept: High
               expectedSorting: []
               requiredSequences: []
@@ -591,19 +591,16 @@ exportCloneGroups:
     - field: -uniqueTagCount
       args:
         - Molecule
-    - field: -targetSequences
-    - field: -targetQualities
     - field: -vHitsWithScore
     - field: -dHitsWithScore
     - field: -jHitsWithScore
     - field: -cHitsWithScore
-    - field: -vAlignments
-    - field: -dAlignments
-    - field: -jAlignments
-    - field: -cAlignments
-    - field: -allNFeaturesWithMinQuality
-    - field: -allAAFeatures
-    - field: -defaultAnchorPoints
+    - field: -nFeature
+      args:
+        - CDR3
+    - field: -aaFeature
+      args:
+        - CDR3
   sortChainsBy: Auto
 qc:
   checks:
@@ -632,3 +629,7 @@ qc:
       upper: 0.2
       middle: 0.1
       label: Reads dropped in tags filtering
+    - type: CellBarcodesWithFoundGroups
+      upper: 0.9
+      middle: 0.8
+      label: Cell barcodes used in result groups
diff --git a/regression/presets/analyze/10x-vdj-bcr-full-length.yaml b/regression/presets/analyze/10x-vdj-bcr-full-length.yaml
@@ -400,7 +400,7 @@ assemble:
                     - allTags:Molecule
               operator:
                 type: group_operator_cumtop
-                share: 0.95
+                share: 0.8
                 accept: High
               expectedSorting:
                 - allTags:Molecule
@@ -429,7 +429,7 @@ assemble:
                   reportHist: null
               operator:
                 type: group_operator_cumtop
-                share: 0.95
+                share: 0.9
                 accept: High
               expectedSorting: []
               requiredSequences: []
@@ -595,19 +595,16 @@ exportCloneGroups:
     - field: -uniqueTagCount
       args:
         - Molecule
-    - field: -targetSequences
-    - field: -targetQualities
     - field: -vHitsWithScore
     - field: -dHitsWithScore
     - field: -jHitsWithScore
     - field: -cHitsWithScore
-    - field: -vAlignments
-    - field: -dAlignments
-    - field: -jAlignments
-    - field: -cAlignments
-    - field: -allNFeaturesWithMinQuality
-    - field: -allAAFeatures
-    - field: -defaultAnchorPoints
+    - field: -nFeature
+      args:
+        - CDR3
+    - field: -aaFeature
+      args:
+        - CDR3
   sortChainsBy: Auto
 qc:
   checks:
@@ -636,3 +633,7 @@ qc:
       upper: 0.2
       middle: 0.1
       label: Reads dropped in tags filtering
+    - type: CellBarcodesWithFoundGroups
+      upper: 0.9
+      middle: 0.8
+      label: Cell barcodes used in result groups
diff --git a/regression/presets/analyze/10x-vdj-bcr.yaml b/regression/presets/analyze/10x-vdj-bcr.yaml
@@ -400,7 +400,7 @@ assemble:
                     - allTags:Molecule
               operator:
                 type: group_operator_cumtop
-                share: 0.95
+                share: 0.8
                 accept: High
               expectedSorting:
                 - allTags:Molecule
@@ -429,7 +429,7 @@ assemble:
                   reportHist: null
               operator:
                 type: group_operator_cumtop
-                share: 0.95
+                share: 0.9
                 accept: High
               expectedSorting: []
               requiredSequences: []
@@ -591,19 +591,16 @@ exportCloneGroups:
     - field: -uniqueTagCount
       args:
         - Molecule
-    - field: -targetSequences
-    - field: -targetQualities
     - field: -vHitsWithScore
     - field: -dHitsWithScore
     - field: -jHitsWithScore
     - field: -cHitsWithScore
-    - field: -vAlignments
-    - field: -dAlignments
-    - field: -jAlignments
-    - field: -cAlignments
-    - field: -allNFeaturesWithMinQuality
-    - field: -allAAFeatures
-    - field: -defaultAnchorPoints
+    - field: -nFeature
+      args:
+        - CDR3
+    - field: -aaFeature
+      args:
+        - CDR3
   sortChainsBy: Auto
 qc:
   checks:
@@ -632,3 +629,7 @@ qc:
       upper: 0.2
       middle: 0.1
       label: Reads dropped in tags filtering
+    - type: CellBarcodesWithFoundGroups
+      upper: 0.9
+      middle: 0.8
+      label: Cell barcodes used in result groups
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
@@ -566,19 +566,16 @@ exportCloneGroups:
     - field: -uniqueTagCount
       args:
         - Molecule
-    - field: -targetSequences
-    - field: -targetQualities
     - field: -vHitsWithScore
     - field: -dHitsWithScore
     - field: -jHitsWithScore
     - field: -cHitsWithScore
-    - field: -vAlignments
-    - field: -dAlignments
-    - field: -jAlignments
-    - field: -cAlignments
-    - field: -allNFeaturesWithMinQuality
-    - field: -allAAFeatures
-    - field: -defaultAnchorPoints
+    - field: -nFeature
+      args:
+        - CDR3
+    - field: -aaFeature
+      args:
+        - CDR3
   sortChainsBy: Auto
 qc:
   checks:
@@ -607,3 +604,7 @@ qc:
       upper: 0.2
       middle: 0.1
       label: Reads dropped in tags filtering
+    - type: CellBarcodesWithFoundGroups
+      upper: 0.9
+      middle: 0.8
+      label: Cell barcodes used in result groups
diff --git a/regression/presets/analyze/10x-vdj-tcr-full-length.yaml b/regression/presets/analyze/10x-vdj-tcr-full-length.yaml
@@ -400,7 +400,7 @@ assemble:
                     - allTags:Molecule
               operator:
                 type: group_operator_cumtop
-                share: 0.95
+                share: 0.8
                 accept: High
               expectedSorting:
                 - allTags:Molecule
@@ -429,7 +429,7 @@ assemble:
                   reportHist: null
               operator:
                 type: group_operator_cumtop
-                share: 0.95
+                share: 0.9
                 accept: High
               expectedSorting: []
               requiredSequences: []
@@ -595,19 +595,16 @@ exportCloneGroups:
     - field: -uniqueTagCount
       args:
         - Molecule
-    - field: -targetSequences
-    - field: -targetQualities
     - field: -vHitsWithScore
     - field: -dHitsWithScore
     - field: -jHitsWithScore
     - field: -cHitsWithScore
-    - field: -vAlignments
-    - field: -dAlignments
-    - field: -jAlignments
-    - field: -cAlignments
-    - field: -allNFeaturesWithMinQuality
-    - field: -allAAFeatures
-    - field: -defaultAnchorPoints
+    - field: -nFeature
+      args:
+        - CDR3
+    - field: -aaFeature
+      args:
+        - CDR3
   sortChainsBy: Auto
 qc:
   checks:
@@ -636,3 +633,7 @@ qc:
       upper: 0.2
       middle: 0.1
       label: Reads dropped in tags filtering
+    - type: CellBarcodesWithFoundGroups
+      upper: 0.9
+      middle: 0.8
+      label: Cell barcodes used in result groups
diff --git a/regression/presets/analyze/10x-vdj-tcr-qc-test.yaml b/regression/presets/analyze/10x-vdj-tcr-qc-test.yaml
@@ -402,7 +402,7 @@ assemble:
                     - allTags:Molecule
               operator:
                 type: group_operator_cumtop
-                share: 0.95
+                share: 0.8
                 accept: High
               expectedSorting:
                 - allTags:Molecule
@@ -431,7 +431,7 @@ assemble:
                   reportHist: null
               operator:
                 type: group_operator_cumtop
-                share: 0.95
+                share: 0.9
                 accept: High
               expectedSorting: []
               requiredSequences: []
@@ -593,19 +593,16 @@ exportCloneGroups:
     - field: -uniqueTagCount
       args:
         - Molecule
-    - field: -targetSequences
-    - field: -targetQualities
     - field: -vHitsWithScore
     - field: -dHitsWithScore
     - field: -jHitsWithScore
     - field: -cHitsWithScore
-    - field: -vAlignments
-    - field: -dAlignments
-    - field: -jAlignments
-    - field: -cAlignments
-    - field: -allNFeaturesWithMinQuality
-    - field: -allAAFeatures
-    - field: -defaultAnchorPoints
+    - field: -nFeature
+      args:
+        - CDR3
+    - field: -aaFeature
+      args:
+        - CDR3
   sortChainsBy: Auto
 qc:
   checks: