working on africapolis workflow

cwl/africapolis/africapolos.cwl

+cwlVersion: v1.2
+class: Workflow
+requirements:
+  - class: InitialWorkDirRequirement
+    listing:
+      - entryname: fishnet
+        writable: true
+        entry: ""
+  - class: ScatterFeatureRequirement
+  - class: StepInputExpressionRequirement
+  - class: InlineJavascriptRequirement
+inputs:
+  vector_input:
+    type: File
+    doc: "Input vector file to Africapolis workflow"
+  config:
+    type: File
+    doc: "Configuration file for Africapolis workflow"
+  partitions:
+    type: int
+    default: 4
+    doc: "Number of partitions created on the input for parallel computation"
+outputs:
+  vector_output:
+    type: File[]
+    outputSource: flatten/flatFiles
+steps:
+  split:
+    run: ../util/split.cwl
+    in:
+      shpFile: vector_input
+      # Pass the relative path "fishnet", which will resolve to the directory created by the InitialWorkDirRequirement.
+      splits: partitions
+    out: [outFile]
+  filter:
+    run: ../sda/filter.cwl
+    in:
+      shpFile:
+        source: split/outFile
+        valueFrom: >
+          $(
+            // self is an array of Files for one shapefile group.
+            // Filter to get those with a basename ending with ".shp" and select the first one.
+            (self.filter(file => file.basename && file.basename.endsWith('.shp')))[0]
+          )
+      config: config
+    scatter: [shpFile]
+    out: [outFile]
+  flatten:
+    run:
+      class: ExpressionTool
+      cwlVersion: v1.2
+      requirements:
+        - class: InlineJavascriptRequirement
+      inputs:
+        files:
+          type:
+            type: array
+            items: 
+              type: array
+              items: File
+      outputs:
+        flatFiles:
+          type: File[]
+      expression: "$( [].concat.apply([], inputs.files) )"
+
+    in:
+      files: filter/outFile
+    out: [flatFiles]
\ No newline at end of file

cwl/africapolis/test-job.json

+{
+    "vector_input":{
+        "class": "File",
+        "path": "/home/lolo/Documents/fishnet/data/samples/Corvara_IT.tiff",
+    },
+    "config":{
+        "class":"File",
+        "path": "/home/lolo/Documents/fishnet/prod/local/sda-workflow-local.json"
+    }
+}
\ No newline at end of file

cwl/types/Shapefile.cwl

+cwlVersion: v1.2
+name: Shapefile
+type: record
+fields:
+  - name: shp
+    type: File
+    doc: "The main Shapefile (.shp)"
+  - name: shx
+    type: File
+    doc: "The shape index file (.shx)"
+  - name: dbf
+    type: File
+    doc: "The attribute data file (.dbf)"
+  - name: prj
+    type: File
+    doc: "The projection file (.prj)"
+  - name: cpg
+    type: File?
+    doc: "The character encoding file (.cpg) (optional)"
+  - name: qpj
+    type: File?
+    doc: "The additional projection file (.qpj) (optional)"