- JD tweak

Author: Alan Christie

data-manager/virtual-screening.yaml

@@ -53,12 +53,12 @@ jobs:
     image:
       name: informaticsmatters/virt-screening-rdkit
       tag: '1.0.0'
-      project-directory: /data
+      project-directory: /home/rdkit/data
     # The command that will be used as the Kubernetes Pod 'command'
     # (after variable expansion). This is a jinja2 template with its variables
     # described in the `variables` block below (A JSONSchema block).
     command: >-
-      python -m shard -i {{ inputFile }} -s {{ supplierName }}
+      python -m shard -i data/{{ inputFile }} -s {{ supplierName }}
       -v {{ supplierVersion }} -o {{ outputDir }} -n {{ codeFieldIndex }}
       --interval 10000
     # Command variables - using JSONSchema to allow for simplified client
@@ -102,13 +102,14 @@ jobs:
         - supplierVersion
         properties:
           codeFieldIndex:
-            default: 1
             title: Index of vendor code field
+            default: 1
             minimum: 0
             type: integer
           outputDir:
             title: Output directory
             type: string
+            default: molecules
           supplierName:
             title: Source of the molecules
             type: string
@@ -126,9 +127,9 @@ jobs:
     image:
       name: informaticsmatters/virt-screening-rdkit
       tag: '1.0.0'
-      project-directory: /data
+      project-directory: /home/rdkit/molecules
     command: >-
-      python -m filter -i {{ inputFile }} -o {{ outputFile }}
+      python -m filter -i molecules/{{ inputFile }} -o {{ outputFile }}
       --min-hac {{ minHac }}
       --max-hac {{ maxHac }}
       --min-rings {{ minRings }}