fix(schema): expand CellRanger parameters

Add support to the config.yaml and its schema validation for the parameter changes imposed by the migration to CellRanger
IMS-Bio2Core-Facility · Dec 9, 2021 · efcd9d8 · efcd9d8
1 parent 4398450
commit efcd9d8
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Showing 2 changed files with 20 additions and 4 deletions.
diff --git a/config/config.yaml b/config/config.yaml
@@ -2,8 +2,8 @@ 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"
+get_cellranger:
+    url: "https://cf.10xgenomics.com/releases/cell-exp/cellranger-6.1.2.tar.gz?Expires=1639086045&Policy=eyJTdGF0ZW1lbnQiOlt7IlJlc291cmNlIjoiaHR0cHM6Ly9jZi4xMHhnZW5vbWljcy5jb20vcmVsZWFzZXMvY2VsbC1leHAvY2VsbHJhbmdlci02LjEuMi50YXIuZ3oiLCJDb25kaXRpb24iOnsiRGF0ZUxlc3NUaGFuIjp7IkFXUzpFcG9jaFRpbWUiOjE2MzkwODYwNDV9fX1dfQ__&Signature=AJxyMHZyneGUVWSaUd2nL2M9BFYNsiVAI157e~8RmO~jV3MNeaXi21gEhXMIiBT6uQOgBkLma7rWCoS99hCI2BivyD~lDCSn3UW4ty-i7EX2P4fdlyJNqz9vGGzbIKClqgocxcQPTIBRTT3NYyG3h8MdrX-k5vgVIrl2kbzIR3wY9RRLe-cYjN3YhA4OLGBTsg7ye7PRRndeJnThEgia4EmYCm29UZ9vHb0sHiGERvQaOBsv9VBvAMrhNkpTSA76Z3iirhZ9ZTza3Vtskp3JVzKLnfAcZukWD10hV2HmTgo0UQX1EN-SAwETemaHZcb7aKAIHIYHQ0nfjVoTVaaV3Q__&Key-Pair-Id=APKAI7S6A5RYOXBWRPDA"
 
 get_gtf:
     url: "http://ftp.ensembl.org/pub/release-104/gtf/mus_musculus/Mus_musculus.GRCm39.104.gtf.gz"
@@ -16,3 +16,8 @@ get_9_to_10:
 
 get_10_to_39:
   url: "http://hgdownload.soe.ucsc.edu/goldenPath/mm10/liftOver/mm10ToMm39.over.chain.gz"
+
+counts:
+  introns: False
+  n_cells: 10000
+  mem: 32
diff --git a/workflow/schema/config.schema.yaml b/workflow/schema/config.schema.yaml
@@ -11,7 +11,7 @@ properties:
     description: PolyA_DB Coordinates
     type: string
 
-  get_whitelist:
+  get_cellranger:
     description: Step Parametres
     type: object
     properties:
@@ -51,11 +51,22 @@ properties:
     required: [ url ]
     additionalProperties: false
 
+  counts:
+    description: Step Parametres
+    type: object
+    properties:
+      introns: { type: boolean }
+      n_cells: { type: integer }
+      mem: { type: integer }
+    required: [ introns, n_cells, mem ]
+    additionalProperties: false
+
 additionalProperties: false
 required:
   - samples
-  - get_whitelist
+  - get_cellranger
   - get_gtf
   - get_fa
   - get_9_to_10
   - get_10_to_39
+  - counts