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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.

id: output-example
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:

id: output-example
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).