From 6f8013187a8117d9d1e49b0412025fe5803d1de5 Mon Sep 17 00:00:00 2001
From: Anh Nguyet Vu <anngvu@gmail.com>
Date: Wed, 6 Sep 2023 08:38:35 -0600
Subject: [PATCH] Add methyl-seq

---
 modules/classes/sequencing.yaml | 80 ++++++++++++++-------------------
 modules/slots.yaml              | 11 ++++-
 2 files changed, 44 insertions(+), 47 deletions(-)

diff --git a/modules/classes/sequencing.yaml b/modules/classes/sequencing.yaml
index 0cfdd33..c571933 100644
--- a/modules/classes/sequencing.yaml
+++ b/modules/classes/sequencing.yaml
@@ -1,7 +1,6 @@
 classes:
   
-  ScRNA-seqLevel1:
-    is_a: SingleCellSequencing
+  Sequencing:
     annotations:
       requiresComponent: ''
       required: false
@@ -12,21 +11,41 @@ classes:
     - ParticipantID
     - SampleID
     - DetailedSampleID
-    - CryopreservedCellsinSample
-    - SingleCellIsolationMethod
-    - DissociationMethod
+    - SequencingPlatform
+    - NucleicAcidSource
     - LibraryConstructionMethod
     - ReadIndicator
     - Read1
     - Read2
+    - TechnicalReplicateGroup
     - EndBias
     - ReverseTranscriptionPrimer
     - SpikeIn
-    - SequencingPlatform
+
+  SingleCellSequencing:
+    is_a: Sequencing
+    annotations:
+      requiresComponent: ''
+      required: false
+    slots:
+    - DissociationMethod
+    - CryopreservedCellsinSample
+    - SingleCellIsolationMethod
     - TotalNumberofInputCells
     - InputCellsandNuclei
-    - ProtocolLink
-    - TechnicalReplicateGroup
+
+  ScRNA-seqLevel1:
+    is_a: SingleCellSequencing
+    annotations:
+      requiresComponent: ''
+      required: false
+    slots:
+    - UMIBarcodeOffset
+    - UMIBarcodeLength
+    - MedianUMIsperCellNumber
+    - CellBarcodeOffset
+    - CellBarcodeLength
+    - ValidBarcodesCellNumber
   
   ScRNA-seqLevel2:
     is_a: SingleCellSequencing
@@ -34,12 +53,6 @@ classes:
       requiresComponent: ''
       required: false
     slots:
-    - Component
-    - Filename
-    - FileFormat
-    - ParticipantID
-    - SampleID
-    - DetailedSampleID
     - ScRNAseqWorkflowType
     - WorkflowVersion
     - ScRNAseqWorkflowParametersDescription
@@ -58,12 +71,6 @@ classes:
       requiresComponent: ''
       required: false
     slots:
-    - Component
-    - Filename
-    - FileFormat
-    - ParticipantID
-    - SampleID
-    - DetailedSampleID
     - DataCategory
     - MatrixType
     - LinkedMatrices
@@ -81,12 +88,6 @@ classes:
       requiresComponent: ''
       required: false
     slots:
-    - Component
-    - Filename
-    - FileFormat
-    - ParticipantID
-    - SampleID
-    - DetailedSampleID
     - DataCategory
     - MatrixType
     - LinkedMatrices
@@ -104,14 +105,6 @@ classes:
       requiresComponent: ''
       required: false
     slots:
-    - Component
-    - Filename
-    - FileFormat
-    - ParticipantID
-    - SampleID
-    - DetailedSampleID
-    - NucleicAcidSource
-    - DissociationMethod
     - SingleNucleusBuffer
     - SingleCellIsolationMethod
     - TranspositionReaction
@@ -123,7 +116,6 @@ classes:
     - ScATACseqRead2
     - ScATACseqRead3
     - LibraryConstructionMethod
-    - SequencingPlatform
     - ThresholdforMinimumPassingReads
     - TotalNumberofPassingNuclei
     - MedianFractionofReadsinPeaks
@@ -134,27 +126,23 @@ classes:
     - TotalReads
     - ProtocolLink
   
-  CEL-seq2:
-    is_a: ScRNA-seqLevel1
+  BulkMethylation-seqLevel1:
+    is_a: Sequencing
     annotations:
       requiresComponent: ''
       required: false
     slots:
-    - EmptyWellBarcode
-    - WellIndex
+    - GenomicCoverageType
+    
   
-  CellBarcodeandUMI:
+  CEL-seq2:
     is_a: ScRNA-seqLevel1
     annotations:
       requiresComponent: ''
       required: false
     slots:
-    - UMIBarcodeOffset
-    - UMIBarcodeLength
-    - MedianUMIsperCellNumber
-    - CellBarcodeOffset
-    - CellBarcodeLength
-    - ValidBarcodesCellNumber
+    - EmptyWellBarcode
+    - WellIndex
   
   MedianFractionofReadsinPeaks:
     is_a: ScATAC-seqLevel1
diff --git a/modules/slots.yaml b/modules/slots.yaml
index 5181901..b55c880 100644
--- a/modules/slots.yaml
+++ b/modules/slots.yaml
@@ -97,8 +97,17 @@ slots:
     required: false
     description: Text term to describe the result of the examination of the breast tissue specimen or fluid as related to the presence and nature of disease.
     annotations:
-      
     range: BreastBiopsyProcedureFindingTypeEnum
+
+  GenomicCoverageType:
+    title: Genomic Coverage Type
+    required: true
+    description: Genomic coverage
+    enum_range: 
+    - Whole Genome
+    - Targeted Genome
+    - Beadchip Array
+
   Laterality:
     title: Sample Laterality
     required: false