Add download surl utils

Former-commit-id: b9599951

steps/create_workflow_input.cwl

+$namespaces:
+  sbg: 'https://www.sevenbridges.com/'
+id: create_workflow_input
+label: create_workflow_input
+class: CommandLineTool
+cwlVersion: v1.0
+inputs: 
+  - id: msin
+    type: Directory[]
+    inputBinding:
+      position: 0
+    
+outputs: 
+  - id: output
+    type: File
+    outputBinding:
+      glob: workflow_input.json
+      
+baseCommand: 
+  - python3
+  - script.py
+doc: ''
+requirements:
+  InitialWorkDirRequirement:
+    listing:
+      - entryname: script.py
+        entry: | 
+          #!/usr/bin/env python3
+          
+          import sys
+          import json
+          import os
+          dir_list = sys.argv[1:]
+          rendered_leafs = []
+          
+          for dir in dir_list:
+              file_name = dir.split(os.path.sep)[-1]
+              rendered_leaf = {'class': 'Directory', 'path': file_name}
+              rendered_leafs.append(rendered_leaf)  
+            
+          with open('workflow_input.json', 'w') as fp:
+              json.dump({'msin': rendered_leafs}, fp)
\ No newline at end of file

steps/read_surl_list.cwl

+class: ExpressionTool
+cwlVersion: v1.0
+id: read_surl_file
+inputs:
+  - id: surl_list
+    type: File
+    doc: input surl file
+    inputBinding:
+      loadContents: True
+outputs:
+  - id: surls
+    type: string[]
+
+expression: |
+  ${
+    var surl_list = inputs.surl_list.contents.split("\n");
+    surl_list = surl_list.filter(function (el) { return el != ''; } );
+    return {'surls': surl_list}
+  }
+label: ReadSurlList
+
+requirements:
+  - class: InlineJavascriptRequirement

steps/surl_copy.cwl

+class: CommandLineTool
+cwlVersion: v1.0
+$namespaces:
+  sbg: 'https://www.sevenbridges.com/'
+id: surl_copy
+baseCommand:
+  - gfal-copy
+inputs:
+  - id: surl
+    type: string
+    inputBinding:
+      position: 0
+outputs:
+  - id: output
+    type: File
+    outputBinding:
+      glob: '*'
+doc: Download a file give a surl
+label: surl_copy

steps/untar.cwl

+id: untar
+label: untar
+class: CommandLineTool
+cwlVersion: v1.0
+inputs: 
+  - id: tar_file
+    type: File
+    inputBinding:
+      position: 0
+    
+outputs: 
+  - id: uncompressed
+    type: Directory
+    outputBinding:
+      glob: 'out/*'
+baseCommand: 
+ - 'bash'
+ - 'untar.sh'
+doc: 'Untar a compressed file'
+requirements:
+  InitialWorkDirRequirement:
+    listing:
+      - entryname: 'untar.sh' 
+        entry: |
+          #!/bin/bash
+          mkdir out
+          cd out
+          tar -xvf $1
+
+    

workflows/dowload_surl_and_create_input_file-json.cwl

+class: Workflow
+cwlVersion: v1.0
+id: dowload_surl_and_create_input_file_json
+label: dowload_surl_and_create_input_file.json
+$namespaces:
+  sbg: 'https://www.sevenbridges.com/'
+inputs:
+  - id: surl_list
+    type: File
+    'sbg:x': -329.7890625
+    'sbg:y': -35
+outputs:
+  - id: msin
+    outputSource:
+      - untar/uncompressed
+    type: Directory
+    'sbg:x': 632
+    'sbg:y': -72
+  - id: workflow_configuration
+    outputSource:
+      - create_workflow_input/output
+    type: File
+    'sbg:x': 663
+    'sbg:y': 137
+steps:
+  - id: read_surl_list
+    in:
+      - id: surl_list
+        source: surl_list
+    out:
+      - id: surls
+    run: ../steps/read_surl_list.cwl
+    label: ReadSurlList
+    'sbg:x': -90
+    'sbg:y': -13
+  - id: surl_copy
+    in:
+      - id: surl
+        source: read_surl_list/surls
+    out:
+      - id: output
+    run: ../steps/surl_copy.cwl
+    label: surl_copy
+    scatter:
+      - surl
+    'sbg:x': 170
+    'sbg:y': -10
+  - id: untar
+    in:
+      - id: tar_file
+        source: surl_copy/output
+    out:
+      - id: uncompressed
+    run: ../steps/untar.cwl
+    label: untar
+    scatter:
+      - tar_file
+    'sbg:x': 376
+    'sbg:y': -12
+  - id: create_workflow_input
+    in:
+      - id: msin
+        source:
+          - untar/uncompressed
+    out:
+      - id: output
+    run: ../steps/create_workflow_input.cwl
+    label: create_workflow_input
+    'sbg:x': 475
+    'sbg:y': 135
+requirements:
+  - class: ScatterFeatureRequirement