new presets for ONT and Pacbio with and without UMI

changelogs/v4.4.2.md

@@ -1,6 +1,8 @@
 ## New features
 
 - Now one can import tags from sequence headers by parsing its content with regular expressions
+- New presets for amplicons/rna-seq sequenced by long-read sequencers such as Pacific Biosciences
+  and Oxford Nanopore: _generic-ont_, _generic-ont-with-umi_, _generic-pacbio_, _generic-pacbio-with-umi_
 
 ## Bug fixes
 

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

@@ -480,3 +480,8 @@ bd-rhapsody-human-bcr-full-length:
 "bd-rhapsody-mouse-bcr-v2":
   deprecation: "The preset is deprecated. Please use bd-mouse-sc-xcr-rhapsody-cdr3."
   inheritFrom:   bd-mouse-sc-xcr-rhapsody-cdr3
+
+# ONT deprecated preset
+"ont-rna-seq":
+  deprecation: "The preset is deprecated. Please use generic-ont."
+  inheritFrom: generic-ont

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

@@ -1,20 +1,62 @@
-"ont-rna-seq":
+"generic-ont":
+  inheritFrom: bundle-base
   flags:
     - species
   pipeline:
     - align
     - assemble
     - assembleContigs
     - exportClones
+  mixins:
+    - type: MaterialTypeRNA
+  align:
+    inheritFrom: align-long-read
+  assemble:
+    inheritFrom: assemble-base
+    overrides:
+      clnaOutput: true
+      cloneAssemblerParameters:
+        badQualityThreshold: 0
+        minimalQuality: 15
+        cloneClusteringParameters:
+          clusteringFilter:
+            type: advanced
+            correctionPower: 0.001
+            backgroundSubstitutionRate: 0.01
+            backgroundIndelRate: 0.01
+  assembleContigs:
+    inheritFrom: assembleContigs-base
+  exportClones:
+    inheritFrom: exportClones-base
   qc:
     checks:
       - type: AlignmentsDroppedLowQuality
         middle: 0.3
         upper: 0.5
+
+"generic-ont-with-umi":
+  inheritFrom: bundle-base
+  flags:
+    - species
+    - tagPattern
+  pipeline:
+    - align
+    - refineTagsAndSort
+    - assemble
+    - assembleContigs
+    - exportClones
+  mixins:
+    - type: MaterialTypeRNA
+    - type: AddTagsValidation
+      validation:
+        type: MustContainTagType
+        tagType: Molecule
   align:
     inheritFrom: align-long-read
+  refineTagsAndSort:
+    inheritFrom: refineTagsAndSort-amplicon-umi-base
   assemble:
-    inheritFrom: assemble-base
+    inheritFrom: assemble-with-consensus-base
     overrides:
       clnaOutput: true
       cloneAssemblerParameters:
@@ -28,7 +70,10 @@
             backgroundIndelRate: 0.01
   assembleContigs:
     inheritFrom: assembleContigs-base
-  exportAlignments:
-    inheritFrom: exportAlignments-base
   exportClones:
-    inheritFrom: exportClones-base
+    inheritFrom: exportClones-umi-base
+  qc:
+    checks:
+      - type: AlignmentsDroppedLowQuality
+        middle: 0.3
+        upper: 0.5

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

@@ -0,0 +1,47 @@
+generic-pacbio:
+  inheritFrom: bundle-base
+  flags:
+    - species
+  pipeline:
+    - align
+    - assemble
+    - exportClones
+  mixins:
+    - type: MaterialTypeRNA
+  align:
+    inheritFrom: align-long-read
+  qc:
+    checks:
+      - type: SuccessfullyAlignedReads
+        middle: 0.7
+        upper: 0.85
+
+generic-pacbio-with-umi:
+  inheritFrom: bundle-base
+  flags:
+    - species
+    - tagPattern
+  pipeline:
+    - align
+    - refineTagsAndSort
+    - assemble
+    - exportClones
+  mixins:
+    - type: MaterialTypeRNA
+    - type: AddTagsValidation
+      validation:
+        type: MustContainTagType
+        tagType: Molecule
+  align:
+    inheritFrom: align-long-read
+  refineTagsAndSort:
+    inheritFrom: refineTagsAndSort-amplicon-umi-base
+  assemble:
+    inheritFrom: assemble-with-consensus-base
+  exportClones:
+    inheritFrom: exportClones-umi-base
+  qc:
+    checks:
+      - type: SuccessfullyAlignedReads
+        middle: 0.7
+        upper: 0.85