Merge pull request #1805 from milaboratory/fix-illumina-layout

Fixed Layout for presets
milaboratory · Sep 27, 2024 · 8b1ab7f · 8b1ab7f
2 parents b4b3d3c + 05b97f9
commit 8b1ab7f
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Showing 57 changed files with 55 additions and 74 deletions.
diff --git a/changelogs/v4.7.1.md b/changelogs/v4.7.1.md
@@ -7,4 +7,5 @@
 
 - Added preset `bruker-human-sc-xcr-vdj-beacon` for TCR/BCR analyses of Bruker Beacon data  
 - Added presets for new Qiagen kits: `qiagen-human-rna-tcr-umi-targeted-qiaseq` and `qiagen-mouse-rna-tcr-umi-targeted-qiaseq`
-- Added preset `illumina-human-dna-trb-ampliseq-sr`
+- Added preset `illumina-human-dna-trb-ampliseq-sr`
+- Removed layout for Illumina kits, iRepertoire and Thermofisher kits.
diff --git a/regression/presets/analyze/ampliseq-tcrb-plus-cdr3.yaml b/regression/presets/analyze/ampliseq-tcrb-plus-cdr3.yaml
@@ -110,7 +110,7 @@ align:
     allowPartialAlignments: false
     allowNoCDR3PartAlignments: false
     allowChimeras: false
-    readsLayout: DirectOnly
+    readsLayout: Opposite
     mergerParameters:
       qualityMergingAlgorithm: MaxSubtraction
       partsLayout: null

diff --git a/regression/presets/analyze/ampliseq-tcrb-plus-full-length.yaml b/regression/presets/analyze/ampliseq-tcrb-plus-full-length.yaml
@@ -110,7 +110,7 @@ align:
     allowPartialAlignments: false
     allowNoCDR3PartAlignments: false
     allowChimeras: false
-    readsLayout: DirectOnly
+    readsLayout: Opposite
     mergerParameters:
       qualityMergingAlgorithm: MaxSubtraction
       partsLayout: null

diff --git a/regression/presets/analyze/ampliseq-tcrb-sr-cdr3.yaml b/regression/presets/analyze/ampliseq-tcrb-sr-cdr3.yaml
@@ -110,7 +110,7 @@ align:
     allowPartialAlignments: false
     allowNoCDR3PartAlignments: false
     allowChimeras: false
-    readsLayout: DirectOnly
+    readsLayout: Opposite
     mergerParameters:
       qualityMergingAlgorithm: MaxSubtraction
       partsLayout: null

diff --git a/regression/presets/analyze/illumina-human-dna-trb-ampliseq-sr.yaml b/regression/presets/analyze/illumina-human-dna-trb-ampliseq-sr.yaml
@@ -110,7 +110,7 @@ align:
     allowPartialAlignments: false
     allowNoCDR3PartAlignments: false
     allowChimeras: false
-    readsLayout: DirectOnly
+    readsLayout: Opposite
     mergerParameters:
       qualityMergingAlgorithm: MaxSubtraction
       partsLayout: null

diff --git a/regression/presets/analyze/illumina-human-rna-trb-ampliseq-plus.yaml b/regression/presets/analyze/illumina-human-rna-trb-ampliseq-plus.yaml
@@ -110,7 +110,7 @@ align:
     allowPartialAlignments: false
     allowNoCDR3PartAlignments: false
     allowChimeras: false
-    readsLayout: DirectOnly
+    readsLayout: Opposite
     mergerParameters:
       qualityMergingAlgorithm: MaxSubtraction
       partsLayout: null

diff --git a/regression/presets/analyze/illumina-human-rna-trb-ampliseq-sr.yaml b/regression/presets/analyze/illumina-human-rna-trb-ampliseq-sr.yaml
@@ -110,7 +110,7 @@ align:
     allowPartialAlignments: false
     allowNoCDR3PartAlignments: false
     allowChimeras: false
-    readsLayout: DirectOnly
+    readsLayout: Opposite
     mergerParameters:
       qualityMergingAlgorithm: MaxSubtraction
       partsLayout: null

diff --git a/regression/presets/analyze/irepertoire-human-dna-igh-lr.yaml b/regression/presets/analyze/irepertoire-human-dna-igh-lr.yaml
@@ -110,7 +110,7 @@ align:
     allowPartialAlignments: false
     allowNoCDR3PartAlignments: false
     allowChimeras: false
-    readsLayout: ReverseOnly
+    readsLayout: Opposite
     mergerParameters:
       qualityMergingAlgorithm: MaxSubtraction
       partsLayout: null

diff --git a/regression/presets/analyze/irepertoire-human-dna-igh-sr.yaml b/regression/presets/analyze/irepertoire-human-dna-igh-sr.yaml
@@ -110,7 +110,7 @@ align:
     allowPartialAlignments: false
     allowNoCDR3PartAlignments: false
     allowChimeras: false
-    readsLayout: ReverseOnly
+    readsLayout: Opposite
     mergerParameters:
       qualityMergingAlgorithm: MaxSubtraction
       partsLayout: null

diff --git a/regression/presets/analyze/irepertoire-human-dna-trb-lr.yaml b/regression/presets/analyze/irepertoire-human-dna-trb-lr.yaml
@@ -110,7 +110,7 @@ align:
     allowPartialAlignments: false
     allowNoCDR3PartAlignments: false
     allowChimeras: false
-    readsLayout: ReverseOnly
+    readsLayout: Opposite
     mergerParameters:
       qualityMergingAlgorithm: MaxSubtraction
       partsLayout: null

diff --git a/regression/presets/analyze/irepertoire-human-dna-trb-sr.yaml b/regression/presets/analyze/irepertoire-human-dna-trb-sr.yaml
@@ -110,7 +110,7 @@ align:
     allowPartialAlignments: false
     allowNoCDR3PartAlignments: false
     allowChimeras: false
-    readsLayout: ReverseOnly
+    readsLayout: Opposite
     mergerParameters:
       qualityMergingAlgorithm: MaxSubtraction
       partsLayout: null

diff --git a/regression/presets/analyze/irepertoire-human-dna-xcr-repseq-lr.yaml b/regression/presets/analyze/irepertoire-human-dna-xcr-repseq-lr.yaml
@@ -110,7 +110,7 @@ align:
     allowPartialAlignments: false
     allowNoCDR3PartAlignments: false
     allowChimeras: false
-    readsLayout: ReverseOnly
+    readsLayout: Opposite
     mergerParameters:
       qualityMergingAlgorithm: MaxSubtraction
       partsLayout: null

diff --git a/regression/presets/analyze/irepertoire-human-dna-xcr-repseq-sr.yaml b/regression/presets/analyze/irepertoire-human-dna-xcr-repseq-sr.yaml
@@ -110,7 +110,7 @@ align:
     allowPartialAlignments: false
     allowNoCDR3PartAlignments: false
     allowChimeras: false
-    readsLayout: ReverseOnly
+    readsLayout: Opposite
     mergerParameters:
       qualityMergingAlgorithm: MaxSubtraction
       partsLayout: null

diff --git a/regression/presets/analyze/irepertoire-human-rna-bcr-lr.yaml b/regression/presets/analyze/irepertoire-human-rna-bcr-lr.yaml
@@ -138,7 +138,7 @@ align:
     allowPartialAlignments: false
     allowNoCDR3PartAlignments: false
     allowChimeras: false
-    readsLayout: ReverseOnly
+    readsLayout: Opposite
     mergerParameters:
       qualityMergingAlgorithm: MaxSubtraction
       partsLayout: null

diff --git a/regression/presets/analyze/irepertoire-human-rna-bcr-sr.yaml b/regression/presets/analyze/irepertoire-human-rna-bcr-sr.yaml
@@ -138,7 +138,7 @@ align:
     allowPartialAlignments: false
     allowNoCDR3PartAlignments: false
     allowChimeras: false
-    readsLayout: ReverseOnly
+    readsLayout: Opposite
     mergerParameters:
       qualityMergingAlgorithm: MaxSubtraction
       partsLayout: null

diff --git a/regression/presets/analyze/irepertoire-human-rna-tcr-lr.yaml b/regression/presets/analyze/irepertoire-human-rna-tcr-lr.yaml
@@ -138,7 +138,7 @@ align:
     allowPartialAlignments: false
     allowNoCDR3PartAlignments: false
     allowChimeras: false
-    readsLayout: ReverseOnly
+    readsLayout: Opposite
     mergerParameters:
       qualityMergingAlgorithm: MaxSubtraction
       partsLayout: null

diff --git a/regression/presets/analyze/irepertoire-human-rna-tcr-sr.yaml b/regression/presets/analyze/irepertoire-human-rna-tcr-sr.yaml
@@ -138,7 +138,7 @@ align:
     allowPartialAlignments: false
     allowNoCDR3PartAlignments: false
     allowChimeras: false
-    readsLayout: ReverseOnly
+    readsLayout: Opposite
     mergerParameters:
       qualityMergingAlgorithm: MaxSubtraction
       partsLayout: null

diff --git a/regression/presets/analyze/irepertoire-human-rna-xcr-repseq-lr.yaml b/regression/presets/analyze/irepertoire-human-rna-xcr-repseq-lr.yaml
@@ -138,7 +138,7 @@ align:
     allowPartialAlignments: false
     allowNoCDR3PartAlignments: false
     allowChimeras: false
-    readsLayout: ReverseOnly
+    readsLayout: Opposite
     mergerParameters:
       qualityMergingAlgorithm: MaxSubtraction
       partsLayout: null

diff --git a/regression/presets/analyze/irepertoire-human-rna-xcr-repseq-plus.yaml b/regression/presets/analyze/irepertoire-human-rna-xcr-repseq-plus.yaml
@@ -138,7 +138,7 @@ align:
     allowPartialAlignments: false
     allowNoCDR3PartAlignments: false
     allowChimeras: false
-    readsLayout: ReverseOnly
+    readsLayout: Opposite
     mergerParameters:
       qualityMergingAlgorithm: MaxSubtraction
       partsLayout: null

diff --git a/regression/presets/analyze/irepertoire-human-rna-xcr-repseq-sr.yaml b/regression/presets/analyze/irepertoire-human-rna-xcr-repseq-sr.yaml
@@ -138,7 +138,7 @@ align:
     allowPartialAlignments: false
     allowNoCDR3PartAlignments: false
     allowChimeras: false
-    readsLayout: ReverseOnly
+    readsLayout: Opposite
     mergerParameters:
       qualityMergingAlgorithm: MaxSubtraction
       partsLayout: null

diff --git a/regression/presets/analyze/irepertoire-mouse-rna-bcr-lr.yaml b/regression/presets/analyze/irepertoire-mouse-rna-bcr-lr.yaml
@@ -138,7 +138,7 @@ align:
     allowPartialAlignments: false
     allowNoCDR3PartAlignments: false
     allowChimeras: false
-    readsLayout: ReverseOnly
+    readsLayout: Opposite
     mergerParameters:
       qualityMergingAlgorithm: MaxSubtraction
       partsLayout: null

diff --git a/regression/presets/analyze/irepertoire-mouse-rna-bcr-sr.yaml b/regression/presets/analyze/irepertoire-mouse-rna-bcr-sr.yaml
@@ -138,7 +138,7 @@ align:
     allowPartialAlignments: false
     allowNoCDR3PartAlignments: false
     allowChimeras: false
-    readsLayout: ReverseOnly
+    readsLayout: Opposite
     mergerParameters:
       qualityMergingAlgorithm: MaxSubtraction
       partsLayout: null

diff --git a/regression/presets/analyze/irepertoire-mouse-rna-tcr-lr.yaml b/regression/presets/analyze/irepertoire-mouse-rna-tcr-lr.yaml
@@ -138,7 +138,7 @@ align:
     allowPartialAlignments: false
     allowNoCDR3PartAlignments: false
     allowChimeras: false
-    readsLayout: ReverseOnly
+    readsLayout: Opposite
     mergerParameters:
       qualityMergingAlgorithm: MaxSubtraction
       partsLayout: null

diff --git a/regression/presets/analyze/irepertoire-mouse-rna-tcr-sr.yaml b/regression/presets/analyze/irepertoire-mouse-rna-tcr-sr.yaml
@@ -138,7 +138,7 @@ align:
     allowPartialAlignments: false
     allowNoCDR3PartAlignments: false
     allowChimeras: false
-    readsLayout: ReverseOnly
+    readsLayout: Opposite
     mergerParameters:
       qualityMergingAlgorithm: MaxSubtraction
       partsLayout: null

diff --git a/regression/presets/analyze/irepertoire-mouse-rna-xcr-repseq-lr.yaml b/regression/presets/analyze/irepertoire-mouse-rna-xcr-repseq-lr.yaml
@@ -138,7 +138,7 @@ align:
     allowPartialAlignments: false
     allowNoCDR3PartAlignments: false
     allowChimeras: false
-    readsLayout: ReverseOnly
+    readsLayout: Opposite
     mergerParameters:
       qualityMergingAlgorithm: MaxSubtraction
       partsLayout: null

diff --git a/regression/presets/analyze/irepertoire-mouse-rna-xcr-repseq-plus.yaml b/regression/presets/analyze/irepertoire-mouse-rna-xcr-repseq-plus.yaml
@@ -138,7 +138,7 @@ align:
     allowPartialAlignments: false
     allowNoCDR3PartAlignments: false
     allowChimeras: false
-    readsLayout: ReverseOnly
+    readsLayout: Opposite
     mergerParameters:
       qualityMergingAlgorithm: MaxSubtraction
       partsLayout: null

diff --git a/regression/presets/analyze/irepertoire-mouse-rna-xcr-repseq-sr.yaml b/regression/presets/analyze/irepertoire-mouse-rna-xcr-repseq-sr.yaml
@@ -138,7 +138,7 @@ align:
     allowPartialAlignments: false
     allowNoCDR3PartAlignments: false
     allowChimeras: false
-    readsLayout: ReverseOnly
+    readsLayout: Opposite
     mergerParameters:
       qualityMergingAlgorithm: MaxSubtraction
       partsLayout: null

diff --git a/regression/presets/analyze/oncomine-human-bcr-ihg-lr-cdr3.yaml b/regression/presets/analyze/oncomine-human-bcr-ihg-lr-cdr3.yaml
@@ -138,7 +138,7 @@ align:
     allowPartialAlignments: false
     allowNoCDR3PartAlignments: false
     allowChimeras: false
-    readsLayout: ReverseOnly
+    readsLayout: Opposite
     mergerParameters:
       qualityMergingAlgorithm: MaxSubtraction
       partsLayout: null

diff --git a/regression/presets/analyze/oncomine-human-bcr-ihg-lr-full-length.yaml b/regression/presets/analyze/oncomine-human-bcr-ihg-lr-full-length.yaml
@@ -138,7 +138,7 @@ align:
     allowPartialAlignments: false
     allowNoCDR3PartAlignments: false
     allowChimeras: false
-    readsLayout: ReverseOnly
+    readsLayout: Opposite
     mergerParameters:
       qualityMergingAlgorithm: MaxSubtraction
       partsLayout: null

diff --git a/regression/presets/analyze/oncomine-human-bcr-pan-clonality-cdr3.yaml b/regression/presets/analyze/oncomine-human-bcr-pan-clonality-cdr3.yaml
@@ -110,7 +110,7 @@ align:
     allowPartialAlignments: false
     allowNoCDR3PartAlignments: false
     allowChimeras: false
-    readsLayout: ReverseOnly
+    readsLayout: Opposite
     mergerParameters:
       qualityMergingAlgorithm: MaxSubtraction
       partsLayout: null

diff --git a/regression/presets/analyze/oncomine-human-igh-fr1-j.yaml b/regression/presets/analyze/oncomine-human-igh-fr1-j.yaml
@@ -110,7 +110,7 @@ align:
     allowPartialAlignments: false
     allowNoCDR3PartAlignments: false
     allowChimeras: false
-    readsLayout: ReverseOnly
+    readsLayout: Opposite
     mergerParameters:
       qualityMergingAlgorithm: MaxSubtraction
       partsLayout: null

diff --git a/regression/presets/analyze/oncomine-human-igh-fr2-j.yaml b/regression/presets/analyze/oncomine-human-igh-fr2-j.yaml
@@ -110,7 +110,7 @@ align:
     allowPartialAlignments: false
     allowNoCDR3PartAlignments: false
     allowChimeras: false
-    readsLayout: ReverseOnly
+    readsLayout: Opposite
     mergerParameters:
       qualityMergingAlgorithm: MaxSubtraction
       partsLayout: null

diff --git a/regression/presets/analyze/oncomine-human-igh-fr3-j.yaml b/regression/presets/analyze/oncomine-human-igh-fr3-j.yaml
@@ -110,7 +110,7 @@ align:
     allowPartialAlignments: false
     allowNoCDR3PartAlignments: false
     allowChimeras: false
-    readsLayout: ReverseOnly
+    readsLayout: Opposite
     mergerParameters:
       qualityMergingAlgorithm: MaxSubtraction
       partsLayout: null

diff --git a/regression/presets/analyze/oncomine-human-igh-leader-j.yaml b/regression/presets/analyze/oncomine-human-igh-leader-j.yaml
@@ -110,7 +110,7 @@ align:
     allowPartialAlignments: false
     allowNoCDR3PartAlignments: false
     allowChimeras: false
-    readsLayout: ReverseOnly
+    readsLayout: Opposite
     mergerParameters:
       qualityMergingAlgorithm: MaxSubtraction
       partsLayout: null

diff --git a/regression/presets/analyze/oncomine-human-tcr-pan-clonality-cdr3.yaml b/regression/presets/analyze/oncomine-human-tcr-pan-clonality-cdr3.yaml
@@ -110,7 +110,7 @@ align:
     allowPartialAlignments: false
     allowNoCDR3PartAlignments: false
     allowChimeras: false
-    readsLayout: ReverseOnly
+    readsLayout: Opposite
     mergerParameters:
       qualityMergingAlgorithm: MaxSubtraction
       partsLayout: null

diff --git a/regression/presets/analyze/oncomine-human-tcrb-lr-cdr3.yaml b/regression/presets/analyze/oncomine-human-tcrb-lr-cdr3.yaml
@@ -138,7 +138,7 @@ align:
     allowPartialAlignments: false
     allowNoCDR3PartAlignments: false
     allowChimeras: false
-    readsLayout: ReverseOnly
+    readsLayout: Opposite
     mergerParameters:
       qualityMergingAlgorithm: MaxSubtraction
       partsLayout: null

diff --git a/regression/presets/analyze/oncomine-human-tcrb-lr-full-length.yaml b/regression/presets/analyze/oncomine-human-tcrb-lr-full-length.yaml
@@ -138,7 +138,7 @@ align:
     allowPartialAlignments: false
     allowNoCDR3PartAlignments: false
     allowChimeras: false
-    readsLayout: ReverseOnly
+    readsLayout: Opposite
     mergerParameters:
       qualityMergingAlgorithm: MaxSubtraction
       partsLayout: null

diff --git a/regression/presets/analyze/oncomine-human-tcrb-sr-cdr3.yaml b/regression/presets/analyze/oncomine-human-tcrb-sr-cdr3.yaml
@@ -110,7 +110,7 @@ align:
     allowPartialAlignments: false
     allowNoCDR3PartAlignments: false
     allowChimeras: false
-    readsLayout: ReverseOnly
+    readsLayout: Opposite
     mergerParameters:
       qualityMergingAlgorithm: MaxSubtraction
       partsLayout: null

diff --git a/regression/presets/analyze/thermofisher-human-dna-bcr-oncomine-pan-clonality.yaml b/regression/presets/analyze/thermofisher-human-dna-bcr-oncomine-pan-clonality.yaml
@@ -110,7 +110,7 @@ align:
     allowPartialAlignments: false
     allowNoCDR3PartAlignments: false
     allowChimeras: false
-    readsLayout: ReverseOnly
+    readsLayout: Opposite
     mergerParameters:
       qualityMergingAlgorithm: MaxSubtraction
       partsLayout: null

diff --git a/regression/presets/analyze/thermofisher-human-dna-igh-oncomine-fr1-j.yaml b/regression/presets/analyze/thermofisher-human-dna-igh-oncomine-fr1-j.yaml
@@ -110,7 +110,7 @@ align:
     allowPartialAlignments: false
     allowNoCDR3PartAlignments: false
     allowChimeras: false
-    readsLayout: ReverseOnly
+    readsLayout: Opposite
     mergerParameters:
       qualityMergingAlgorithm: MaxSubtraction
       partsLayout: null

diff --git a/regression/presets/analyze/thermofisher-human-dna-igh-oncomine-fr2-j.yaml b/regression/presets/analyze/thermofisher-human-dna-igh-oncomine-fr2-j.yaml
@@ -110,7 +110,7 @@ align:
     allowPartialAlignments: false
     allowNoCDR3PartAlignments: false
     allowChimeras: false
-    readsLayout: ReverseOnly
+    readsLayout: Opposite
     mergerParameters:
       qualityMergingAlgorithm: MaxSubtraction
       partsLayout: null

diff --git a/regression/presets/analyze/thermofisher-human-dna-igh-oncomine-fr3-j.yaml b/regression/presets/analyze/thermofisher-human-dna-igh-oncomine-fr3-j.yaml
@@ -110,7 +110,7 @@ align:
     allowPartialAlignments: false
     allowNoCDR3PartAlignments: false
     allowChimeras: false
-    readsLayout: ReverseOnly
+    readsLayout: Opposite
     mergerParameters:
       qualityMergingAlgorithm: MaxSubtraction
       partsLayout: null

diff --git a/regression/presets/analyze/thermofisher-human-dna-igh-oncomine-sr.yaml b/regression/presets/analyze/thermofisher-human-dna-igh-oncomine-sr.yaml
@@ -110,7 +110,7 @@ align:
     allowPartialAlignments: false
     allowNoCDR3PartAlignments: false
     allowChimeras: false
-    readsLayout: ReverseOnly
+    readsLayout: Opposite
     mergerParameters:
       qualityMergingAlgorithm: MaxSubtraction
       partsLayout: null

diff --git a/regression/presets/analyze/thermofisher-human-dna-igh-oncomine-v-leader-j.yaml b/regression/presets/analyze/thermofisher-human-dna-igh-oncomine-v-leader-j.yaml
@@ -110,7 +110,7 @@ align:
     allowPartialAlignments: false
     allowNoCDR3PartAlignments: false
     allowChimeras: false
-    readsLayout: ReverseOnly
+    readsLayout: Opposite
     mergerParameters:
       qualityMergingAlgorithm: MaxSubtraction
       partsLayout: null