feat(schemas): provide validation for lift.yaml

Provides a lift.yaml file and apropriate schema validation for it.

config/config.yaml

@@ -1,5 +1,7 @@
 samples: "config/samples.yaml"
 
+lift: "config/lift.yaml"
+
 get_whitelist:
     url: "https://github.com/10XGenomics/cellranger/raw/master/lib/python/cellranger/barcodes/3M-february-2018.txt.gz"
 

config/lift.yaml

@@ -0,0 +1,4 @@
+Glp1r:
+  chr: 17
+  start: 31038812
+  end: 31078178

workflow/rules/common.smk

@@ -5,7 +5,12 @@ from yaml import safe_load
 # Validate structures
 with open(config["samples"], "r") as file:
     metadata = safe_load(file)
-validate(metadata, schema="../schema/samples.schema.yaml")
+    validate(metadata, schema="../schema/samples.schema.yaml")
+
+with open(config["lift"], "r") as file:
+    lift = safe_load(file)
+    validate(lift, schema="../schema/lift.schema.yaml")
+
 validate(config, schema="../schema/config.schema.yaml")
 
 # Some useful variables

workflow/schema/config.schema.yaml

@@ -7,6 +7,10 @@ properties:
     description: Samplesheet location
     type: string
 
+  lift:
+    description: PolyA_DB Coordinates
+    type: string
+
   get_whitelist:
     description: Step Parametres
     type: object

workflow/schema/lift.schema.yaml

@@ -0,0 +1,20 @@
+$schema: "http://json-schema.org/draft-07/schema#"
+
+description: Sample File Schema
+
+additionalProperties: false
+patternProperties:
+  ^[^\W_]*$:
+    description: Gene Symbol
+    type: object
+    additionalProperties: false
+    properties:
+      chr:
+        description: Chromosome number
+        type: integer
+      start:
+        description: Start coordinate, 1-indexed
+        type: integer
+      end:
+        description: End Coordinate, 1-indexed
+        type: integer