Working on #16 #7 & code cleanup

Tuks-ICMM · Oct 29, 2021 · e6f4de5 · e6f4de5
1 parent 57860cb
commit e6f4de5
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Showing 9 changed files with 5,145 additions and 65 deletions.
diff --git a/config/config.schema.json → config/.schemas/config.schema.json b/config/config.schema.json → config/.schemas/config.schema.json
diff --git a/config/.schemas/pep.schema.yaml b/config/.schemas/pep.schema.yaml
@@ -0,0 +1,15 @@
+$schema: "https://json-schema.org/draft-06/schema#"
+description: A single sample used in this analysis, as provided in the PEP sample sheet
+properties:
+  sample_name:
+    type: string
+    description: Sample identifier
+  dataset:
+    type: string
+    description: A string identifier indicating the name of the dataset. This will be used to name the output.
+  file:
+    type: string
+    decription: A string filename for the data file (.vcf.gz + tabix) in the input folder.
+  reference_genome:
+    type: string
+    description: A string identifier for the reference genome. This will be used to access a correspondingly named FATSA file in the resources folder.
diff --git a/config/Clusters.xlsx b/config/Clusters.xlsx
diff --git a/config/config.json b/config/config.json
@@ -75,9 +75,42 @@
     "working-directory": "/nlustre/users/graeme/pipeline-2020",
     "queues": [
       {
-        "name": "long",
+        "queue": "long",
         "walltime": "900:00:00",
-        "memory": "128G"
+        "memory": "128G",
+        "cores": 10,
+        "nodes": 1,
+        "rules": [
+          "VALIDATE",
+          "LIFTOVER",
+          "ANNOTATE",
+          "ADMIXTURE",
+          "COLLATE"
+        ]
+      },
+      {
+        "queue": "normal",
+        "walltime": "30:00:00",
+        "memory": "128G",
+        "cores": 10,
+        "nodes": 1,
+        "rules": [
+          "TRIM_AND_NAME",
+          "TRANSPILE_CLUSTERS",
+          "PLINK",
+          "CALCULATIONS",
+          "COMPILE_EXCEL"
+        ]
+      },
+      {
+        "queue": "short",
+        "walltime": "00:30:00",
+        "memory": "128G",
+        "cores": 10,
+        "nodes": 1,
+        "rules": [
+          "FILTER"
+        ]
       }
     ]
   }