Outputs

Output parameters can be used as placeholders for folders or files which are created by steps. Cloudgene supports POSIX compatible filesystems (e.g. Linux or OS X) and the Hadoop Distributed File System (HDFS). Cloudgene creates and manages these folders for you as well as enables downloading the files through the web interface.

Output parameters are defined in the outputs section where each parameter is defined by an unique id, a textual description and a type.

name: output-example
version: 1.0
workflow:
  outputs:
    - id: output
      description: Output Folder
      type: local_folder
      mergeOutput: false
      download: true
      zip: false

The value of the parameter can be referenced by $id in the workflow. In this example, we use the touch command to create a file in an output folder:

name: output-example
version: 1.0
workflow:
  steps:
    - name: Name Step1
      cmd: /bin/touch $output/new-file.txt
  outputs:
    - id: output
      description: Output Folder
      type: local_folder
      mergeOutput: false
      download: true
      zip: false

Properties

These properties define the basic behaviour of an output parameter:

Property Required Description
id yes Defines a id for the parameter
description yes Defines a description for the parameter
type yes One of the following types
download no If download is set to true, the file or folder can be downloaded (default: true).
adminOnly no (default: false).

Types

At the moment the following types of output parameters are supported:

local_file

local_folder

hdfs_file

Property Required Description
zip no If zip is set to true, all files in a hdfs-folder or local-folder are automatically compressed into a zip file (default: true).

hdfs_folder

Property Required Description
mergeOutput no If mergeOutput is set to true, all files in a hdfs-folder are merged into a single file (default: true).
zip no If zip is set to true, all files in a hdfs-folder or local-folder are automatically compressed into a zip file (default: true).
removeHeader no If removeHeader is set to true, the header of each file is removed and the merged file has a single header. default: true).