added presets for BIOMED2 IGK/IGL and TRB/TRD/TRG

changelogs/v4.4.md

@@ -42,6 +42,8 @@
 
 - Parse bio preset has been corrected and now includes the whitelists for all CELL barcodes. CELL1, CELL2 and CELL3 now correspond to ParseBio Round 1, Round 2 and Round 3. Original Parse Bio cell barcodes naming has been added.
 
+- Two new presets for BIOMED2 added primer set added: `biomed2-human-igl-igk`, `biomed2-human-trb-trd-trg`.
+
 - kAligner2 has been modified to work with both TCR and BCR data, the presets previously divided by the type of data now merged into one. Also, the division by `cdr3` and `full-length` presets has been deprecated; now the presets by default use the longest possible assembling feature according to the protocol:
 
   - Generic amplicon presets `generic-tcr-amplicon`, `generic-bcr-amplicon`, `generic-tcr-amplicon-umi` and `generic-bcr-amplicon-umi` are depricated. New generic amplicon presets: `generic-amplicon` and `generic-amplicon-with-umi`
@@ -58,7 +60,7 @@
 
   - `takara-mouse-tcr-cdr3` and `takara-mouse-tcr-full-length` are deprecated and replaced by `takara-mouse-tcr-profiling` with assembling feature `{VDJRegion}`
 
-  - `biomed2-human-bcr-cdr3` and `biomed2-human-bcr-full-length` are deprecated and replaced by `biomed2-human-bcr` with assembling feature `{CDR1Begin:CDR3End}`
+  - `biomed2-human-bcr-cdr3` and `biomed2-human-bcr-full-length` are deprecated and replaced by `biomed2-human-igh` with assembling feature `{CDR1Begin:CDR3End}`
 
   - `ampliseq-tcrb-sr-cdr3` has been deprecated and replaced with `ampliseq-tcrb-sr`
 

src/main/resources/presets/protocols/biomed2.yaml

@@ -1,4 +1,4 @@
-"biomed2-human-bcr":
+"biomed2-human-igh":
   inheritFrom: generic-amplicon
   pipeline:
     - align
@@ -18,4 +18,36 @@
       geneType: J
     - type: MaterialTypeRNA
 
+"biomed2-human-igl-igk":
+  inheritFrom: generic-amplicon
+  pipeline:
+    - align
+    - assemble
+    - exportClones
+  mixins:
+    - type: SetSpecies
+      species: hs
+    - type: LeftAlignmentBoundaryNoPoint
+      floating: true
+    - type: RightAlignmentBoundaryNoPoint
+      floating: true
+      geneType: J
+    - type: MaterialTypeRNA
+
+"biomed2-human-trb-trd-trg":
+  inheritFrom: generic-amplicon
+  pipeline:
+    - align
+    - assemble
+    - exportClones
+  mixins:
+    - type: SetSpecies
+      species: hs
+    - type: LeftAlignmentBoundaryNoPoint
+      floating: true
+    - type: RightAlignmentBoundaryNoPoint
+      floating: true
+      geneType: J
+    - type: MaterialTypeRNA
+
 

src/main/resources/presets/protocols/legacy.yaml

@@ -101,15 +101,15 @@ abhelix-human-tcr-full-length:
 # Biomed2 deprecated presets
 
 biomed2-human-bcr-cdr3:
-  deprecation: "The preset is deprecated. Please use biomed2-human-bcr. Notice that by default clones will be assembled by {CDR1Begin:CDR3End}, to mimic the behavior of the current deprecated preset add --assemble-contigs-by CDR3"
-  inheritFrom: biomed2-human-bcr
+  deprecation: "The preset is deprecated. Please use biomed2-human-igh. Notice that by default clones will be assembled by {CDR1Begin:CDR3End}, to mimic the behavior of the current deprecated preset add --assemble-contigs-by CDR3"
+  inheritFrom: biomed2-human-igh
   mixins:
     - type: SetClonotypeAssemblingFeatures
       features: [ "CDR3" ]
 
 biomed2-human-bcr-full-length:
-  deprecation: "The preset is deprecated. Please use biomed2-human-bcr."
-  inheritFrom: biomed2-human-bcr
+  deprecation: "The preset is deprecated. Please use biomed2-human-igh."
+  inheritFrom: biomed2-human-igh
 
 # Illumina deprecated presets