Merge pull request #1495 from milaboratory/presets-adjustment

Presets adjustment. Removed split by V and J for Full Length presets
milaboratory · Jan 3, 2024 · 53be159 · 53be159
2 parents e42a6b2 + e1f558b
commit 53be159
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Showing 42 changed files with 77 additions and 106 deletions.
diff --git a/changelogs/v4.6.1.md b/changelogs/v4.6.1.md
@@ -12,3 +12,4 @@
 - Fixed usage `--remove-step qc`
 - Added `--remove-qc-check` option
 - Remove `-topChains` field from `exportShmTreesWithNodes` command. Use `-chains` instead
+- Removed default splitting clones by V and J for presets where clones are assembled by full-length.
diff --git a/regression/presets/analyze/neb-human-rna-xcr-umi-nebnext.yaml b/regression/presets/analyze/neb-human-rna-xcr-umi-nebnext.yaml
@@ -292,8 +292,8 @@ assemble:
         absoluteMinScore: null
         maxHits: null
         scoring: null
-    separateByV: true
-    separateByJ: true
+    separateByV: false
+    separateByJ: false
     separateByC: true
     maximalPreClusteringRatio: 1.0
     preClusteringScoreFilteringRatio: 2.0

diff --git a/regression/presets/analyze/neb-mouse-rna-xcr-umi-nebnext.yaml b/regression/presets/analyze/neb-mouse-rna-xcr-umi-nebnext.yaml
@@ -292,8 +292,8 @@ assemble:
         absoluteMinScore: null
         maxHits: null
         scoring: null
-    separateByV: true
-    separateByJ: true
+    separateByV: false
+    separateByJ: false
     separateByC: true
     maximalPreClusteringRatio: 1.0
     preClusteringScoreFilteringRatio: 2.0

diff --git a/regression/presets/analyze/nebnext-human-bcr-cdr3.yaml b/regression/presets/analyze/nebnext-human-bcr-cdr3.yaml
@@ -292,8 +292,8 @@ assemble:
         absoluteMinScore: null
         maxHits: null
         scoring: null
-    separateByV: true
-    separateByJ: true
+    separateByV: false
+    separateByJ: false
     separateByC: true
     maximalPreClusteringRatio: 1.0
     preClusteringScoreFilteringRatio: 2.0

diff --git a/regression/presets/analyze/nebnext-human-bcr-full-length.yaml b/regression/presets/analyze/nebnext-human-bcr-full-length.yaml
@@ -292,8 +292,8 @@ assemble:
         absoluteMinScore: null
         maxHits: null
         scoring: null
-    separateByV: true
-    separateByJ: true
+    separateByV: false
+    separateByJ: false
     separateByC: true
     maximalPreClusteringRatio: 1.0
     preClusteringScoreFilteringRatio: 2.0

diff --git a/regression/presets/analyze/nebnext-human-tcr-bcr-cdr3.yaml b/regression/presets/analyze/nebnext-human-tcr-bcr-cdr3.yaml
@@ -292,8 +292,8 @@ assemble:
         absoluteMinScore: null
         maxHits: null
         scoring: null
-    separateByV: true
-    separateByJ: true
+    separateByV: false
+    separateByJ: false
     separateByC: true
     maximalPreClusteringRatio: 1.0
     preClusteringScoreFilteringRatio: 2.0

diff --git a/regression/presets/analyze/nebnext-human-tcr-bcr-full-length.yaml b/regression/presets/analyze/nebnext-human-tcr-bcr-full-length.yaml
@@ -292,8 +292,8 @@ assemble:
         absoluteMinScore: null
         maxHits: null
         scoring: null
-    separateByV: true
-    separateByJ: true
+    separateByV: false
+    separateByJ: false
     separateByC: true
     maximalPreClusteringRatio: 1.0
     preClusteringScoreFilteringRatio: 2.0

diff --git a/regression/presets/analyze/nebnext-human-tcr-cdr3.yaml b/regression/presets/analyze/nebnext-human-tcr-cdr3.yaml
@@ -292,8 +292,8 @@ assemble:
         absoluteMinScore: null
         maxHits: null
         scoring: null
-    separateByV: true
-    separateByJ: true
+    separateByV: false
+    separateByJ: false
     separateByC: true
     maximalPreClusteringRatio: 1.0
     preClusteringScoreFilteringRatio: 2.0

diff --git a/regression/presets/analyze/nebnext-human-tcr-full-length.yaml b/regression/presets/analyze/nebnext-human-tcr-full-length.yaml
@@ -292,8 +292,8 @@ assemble:
         absoluteMinScore: null
         maxHits: null
         scoring: null
-    separateByV: true
-    separateByJ: true
+    separateByV: false
+    separateByJ: false
     separateByC: true
     maximalPreClusteringRatio: 1.0
     preClusteringScoreFilteringRatio: 2.0

diff --git a/regression/presets/analyze/nebnext-mouse-bcr-cdr3.yaml b/regression/presets/analyze/nebnext-mouse-bcr-cdr3.yaml
@@ -292,8 +292,8 @@ assemble:
         absoluteMinScore: null
         maxHits: null
         scoring: null
-    separateByV: true
-    separateByJ: true
+    separateByV: false
+    separateByJ: false
     separateByC: true
     maximalPreClusteringRatio: 1.0
     preClusteringScoreFilteringRatio: 2.0

diff --git a/regression/presets/analyze/nebnext-mouse-bcr-full-length.yaml b/regression/presets/analyze/nebnext-mouse-bcr-full-length.yaml
@@ -292,8 +292,8 @@ assemble:
         absoluteMinScore: null
         maxHits: null
         scoring: null
-    separateByV: true
-    separateByJ: true
+    separateByV: false
+    separateByJ: false
     separateByC: true
     maximalPreClusteringRatio: 1.0
     preClusteringScoreFilteringRatio: 2.0

diff --git a/regression/presets/analyze/nebnext-mouse-tcr-bcr-cdr3.yaml b/regression/presets/analyze/nebnext-mouse-tcr-bcr-cdr3.yaml
@@ -292,8 +292,8 @@ assemble:
         absoluteMinScore: null
         maxHits: null
         scoring: null
-    separateByV: true
-    separateByJ: true
+    separateByV: false
+    separateByJ: false
     separateByC: true
     maximalPreClusteringRatio: 1.0
     preClusteringScoreFilteringRatio: 2.0

diff --git a/regression/presets/analyze/nebnext-mouse-tcr-bcr-full-length.yaml b/regression/presets/analyze/nebnext-mouse-tcr-bcr-full-length.yaml
@@ -292,8 +292,8 @@ assemble:
         absoluteMinScore: null
         maxHits: null
         scoring: null
-    separateByV: true
-    separateByJ: true
+    separateByV: false
+    separateByJ: false
     separateByC: true
     maximalPreClusteringRatio: 1.0
     preClusteringScoreFilteringRatio: 2.0

diff --git a/regression/presets/analyze/nebnext-mouse-tcr-cdr3.yaml b/regression/presets/analyze/nebnext-mouse-tcr-cdr3.yaml
@@ -292,8 +292,8 @@ assemble:
         absoluteMinScore: null
         maxHits: null
         scoring: null
-    separateByV: true
-    separateByJ: true
+    separateByV: false
+    separateByJ: false
     separateByC: true
     maximalPreClusteringRatio: 1.0
     preClusteringScoreFilteringRatio: 2.0

diff --git a/regression/presets/analyze/nebnext-mouse-tcr-full-length.yaml b/regression/presets/analyze/nebnext-mouse-tcr-full-length.yaml
@@ -292,8 +292,8 @@ assemble:
         absoluteMinScore: null
         maxHits: null
         scoring: null
-    separateByV: true
-    separateByJ: true
+    separateByV: false
+    separateByJ: false
     separateByC: true
     maximalPreClusteringRatio: 1.0
     preClusteringScoreFilteringRatio: 2.0

diff --git a/regression/presets/analyze/qiagen-human-rna-tcr-umi-qiaseq.yaml b/regression/presets/analyze/qiagen-human-rna-tcr-umi-qiaseq.yaml
@@ -307,8 +307,8 @@ assemble:
         absoluteMinScore: null
         maxHits: null
         scoring: null
-    separateByV: true
-    separateByJ: true
+    separateByV: false
+    separateByJ: false
     separateByC: true
     maximalPreClusteringRatio: 1.0
     preClusteringScoreFilteringRatio: 2.0

diff --git a/regression/presets/analyze/qiagen-mouse-rna-tcr-umi-qiaseq.yaml b/regression/presets/analyze/qiagen-mouse-rna-tcr-umi-qiaseq.yaml
@@ -307,8 +307,8 @@ assemble:
         absoluteMinScore: null
         maxHits: null
         scoring: null
-    separateByV: true
-    separateByJ: true
+    separateByV: false
+    separateByJ: false
     separateByC: true
     maximalPreClusteringRatio: 1.0
     preClusteringScoreFilteringRatio: 2.0

diff --git a/regression/presets/analyze/qiaseq-human-tcr-cdr3.yaml b/regression/presets/analyze/qiaseq-human-tcr-cdr3.yaml
@@ -307,8 +307,8 @@ assemble:
         absoluteMinScore: null
         maxHits: null
         scoring: null
-    separateByV: true
-    separateByJ: true
+    separateByV: false
+    separateByJ: false
     separateByC: true
     maximalPreClusteringRatio: 1.0
     preClusteringScoreFilteringRatio: 2.0

diff --git a/regression/presets/analyze/qiaseq-human-tcr-full-length.yaml b/regression/presets/analyze/qiaseq-human-tcr-full-length.yaml
@@ -307,8 +307,8 @@ assemble:
         absoluteMinScore: null
         maxHits: null
         scoring: null
-    separateByV: true
-    separateByJ: true
+    separateByV: false
+    separateByJ: false
     separateByC: true
     maximalPreClusteringRatio: 1.0
     preClusteringScoreFilteringRatio: 2.0

diff --git a/regression/presets/analyze/qiaseq-mouse-tcr-cdr3.yaml b/regression/presets/analyze/qiaseq-mouse-tcr-cdr3.yaml
@@ -307,8 +307,8 @@ assemble:
         absoluteMinScore: null
         maxHits: null
         scoring: null
-    separateByV: true
-    separateByJ: true
+    separateByV: false
+    separateByJ: false
     separateByC: true
     maximalPreClusteringRatio: 1.0
     preClusteringScoreFilteringRatio: 2.0

diff --git a/regression/presets/analyze/qiaseq-mouse-tcr-full-length.yaml b/regression/presets/analyze/qiaseq-mouse-tcr-full-length.yaml
@@ -307,8 +307,8 @@ assemble:
         absoluteMinScore: null
         maxHits: null
         scoring: null
-    separateByV: true
-    separateByJ: true
+    separateByV: false
+    separateByJ: false
     separateByC: true
     maximalPreClusteringRatio: 1.0
     preClusteringScoreFilteringRatio: 2.0

diff --git a/regression/presets/analyze/takara-human-bcr-cdr3.yaml b/regression/presets/analyze/takara-human-bcr-cdr3.yaml
@@ -292,8 +292,8 @@ assemble:
         absoluteMinScore: null
         maxHits: null
         scoring: null
-    separateByV: true
-    separateByJ: true
+    separateByV: false
+    separateByJ: false
     separateByC: true
     maximalPreClusteringRatio: 1.0
     preClusteringScoreFilteringRatio: 2.0

diff --git a/regression/presets/analyze/takara-human-bcr-full-length.yaml b/regression/presets/analyze/takara-human-bcr-full-length.yaml
@@ -292,8 +292,8 @@ assemble:
         absoluteMinScore: null
         maxHits: null
         scoring: null
-    separateByV: true
-    separateByJ: true
+    separateByV: false
+    separateByJ: false
     separateByC: true
     maximalPreClusteringRatio: 1.0
     preClusteringScoreFilteringRatio: 2.0

diff --git a/regression/presets/analyze/takara-human-rna-bcr-umi-smarter.yaml b/regression/presets/analyze/takara-human-rna-bcr-umi-smarter.yaml
@@ -292,8 +292,8 @@ assemble:
         absoluteMinScore: null
         maxHits: null
         scoring: null
-    separateByV: true
-    separateByJ: true
+    separateByV: false
+    separateByJ: false
     separateByC: true
     maximalPreClusteringRatio: 1.0
     preClusteringScoreFilteringRatio: 2.0

diff --git a/regression/presets/analyze/takara-human-rna-bcr-umi-smartseq.yaml b/regression/presets/analyze/takara-human-rna-bcr-umi-smartseq.yaml
@@ -292,8 +292,8 @@ assemble:
         absoluteMinScore: null
         maxHits: null
         scoring: null
-    separateByV: true
-    separateByJ: true
+    separateByV: false
+    separateByJ: false
     separateByC: true
     maximalPreClusteringRatio: 1.0
     preClusteringScoreFilteringRatio: 2.0

diff --git a/regression/presets/analyze/takara-human-rna-tcr-smarter.yaml b/regression/presets/analyze/takara-human-rna-tcr-smarter.yaml
@@ -230,8 +230,8 @@ assemble:
         absoluteMinScore: null
         maxHits: null
         scoring: null
-    separateByV: true
-    separateByJ: true
+    separateByV: false
+    separateByJ: false
     separateByC: true
     maximalPreClusteringRatio: 1.0
     preClusteringScoreFilteringRatio: 2.0

diff --git a/regression/presets/analyze/takara-human-rna-tcr-umi-smarter-v2.yaml b/regression/presets/analyze/takara-human-rna-tcr-umi-smarter-v2.yaml
@@ -292,8 +292,8 @@ assemble:
         absoluteMinScore: null
         maxHits: null
         scoring: null
-    separateByV: true
-    separateByJ: true
+    separateByV: false
+    separateByJ: false
     separateByC: true
     maximalPreClusteringRatio: 1.0
     preClusteringScoreFilteringRatio: 2.0

diff --git a/regression/presets/analyze/takara-human-rna-tcr-umi-smartseq.yaml b/regression/presets/analyze/takara-human-rna-tcr-umi-smartseq.yaml
@@ -292,8 +292,8 @@ assemble:
         absoluteMinScore: null
         maxHits: null
         scoring: null
-    separateByV: true
-    separateByJ: true
+    separateByV: false
+    separateByJ: false
     separateByC: true
     maximalPreClusteringRatio: 1.0
     preClusteringScoreFilteringRatio: 2.0

diff --git a/regression/presets/analyze/takara-human-tcr-V1-cdr3.yaml b/regression/presets/analyze/takara-human-tcr-V1-cdr3.yaml
@@ -230,8 +230,8 @@ assemble:
         absoluteMinScore: null
         maxHits: null
         scoring: null
-    separateByV: true
-    separateByJ: true
+    separateByV: false
+    separateByJ: false
     separateByC: true
     maximalPreClusteringRatio: 1.0
     preClusteringScoreFilteringRatio: 2.0

diff --git a/regression/presets/analyze/takara-human-tcr-V1-full-length.yaml b/regression/presets/analyze/takara-human-tcr-V1-full-length.yaml
@@ -230,8 +230,8 @@ assemble:
         absoluteMinScore: null
         maxHits: null
         scoring: null
-    separateByV: true
-    separateByJ: true
+    separateByV: false
+    separateByJ: false
     separateByC: true
     maximalPreClusteringRatio: 1.0
     preClusteringScoreFilteringRatio: 2.0

diff --git a/regression/presets/analyze/takara-human-tcr-V2-cdr3.yaml b/regression/presets/analyze/takara-human-tcr-V2-cdr3.yaml
@@ -292,8 +292,8 @@ assemble:
         absoluteMinScore: null
         maxHits: null
         scoring: null
-    separateByV: true
-    separateByJ: true
+    separateByV: false
+    separateByJ: false
     separateByC: true
     maximalPreClusteringRatio: 1.0
     preClusteringScoreFilteringRatio: 2.0

diff --git a/regression/presets/analyze/takara-human-tcr-V2-full-length.yaml b/regression/presets/analyze/takara-human-tcr-V2-full-length.yaml
@@ -292,8 +292,8 @@ assemble:
         absoluteMinScore: null
         maxHits: null
         scoring: null
-    separateByV: true
-    separateByJ: true
+    separateByV: false
+    separateByJ: false
     separateByC: true
     maximalPreClusteringRatio: 1.0
     preClusteringScoreFilteringRatio: 2.0

diff --git a/regression/presets/analyze/takara-mouse-bcr-cdr3.yaml b/regression/presets/analyze/takara-mouse-bcr-cdr3.yaml
@@ -230,8 +230,8 @@ assemble:
         absoluteMinScore: null
         maxHits: null
         scoring: null
-    separateByV: true
-    separateByJ: true
+    separateByV: false
+    separateByJ: false
     separateByC: true
     maximalPreClusteringRatio: 1.0
     preClusteringScoreFilteringRatio: 2.0

diff --git a/regression/presets/analyze/takara-mouse-bcr-full-length.yaml b/regression/presets/analyze/takara-mouse-bcr-full-length.yaml
@@ -230,8 +230,8 @@ assemble:
         absoluteMinScore: null
         maxHits: null
         scoring: null
-    separateByV: true
-    separateByJ: true
+    separateByV: false
+    separateByJ: false
     separateByC: true
     maximalPreClusteringRatio: 1.0
     preClusteringScoreFilteringRatio: 2.0

diff --git a/regression/presets/analyze/takara-mouse-rna-bcr-smarter.yaml b/regression/presets/analyze/takara-mouse-rna-bcr-smarter.yaml
@@ -230,8 +230,8 @@ assemble:
         absoluteMinScore: null
         maxHits: null
         scoring: null
-    separateByV: true
-    separateByJ: true
+    separateByV: false
+    separateByJ: false
     separateByC: true
     maximalPreClusteringRatio: 1.0
     preClusteringScoreFilteringRatio: 2.0

diff --git a/regression/presets/analyze/takara-mouse-rna-tcr-smarter.yaml b/regression/presets/analyze/takara-mouse-rna-tcr-smarter.yaml
@@ -230,8 +230,8 @@ assemble:
         absoluteMinScore: null
         maxHits: null
         scoring: null
-    separateByV: true
-    separateByJ: true
+    separateByV: false
+    separateByJ: false
     separateByC: true
     maximalPreClusteringRatio: 1.0
     preClusteringScoreFilteringRatio: 2.0