read_object | WDL Specification

Object read_object(File)

Reads a tab-separated value (TSV) file representing the names and values of the members of an Object. There must be exactly two rows, and each row must have the same number of elements, otherwise an error is raised. Trailing end-of-line characters (\r and \n) are removed from each line.

The first row specifies the object member names. The names in the first row must be unique; if there are any duplicate names, an error is raised.

The second row specifies the object member values corresponding to the names in the first row. All of the Object's values are of type String.

Parameters

File: Path of the two-row TSV file to read.

Returns: An Object, with as many members as there are unique names in the TSV.

Example: read_object_task.wdl

version 1.2

task read_object {
  command <<<
    python <<CODE
    print('\t'.join(["key_{}".format(i) for i in range(3)]))
    print('\t'.join(["value_{}".format(i) for i in range(3)]))
    CODE
  >>>

  output {
    Object my_obj = read_object(stdout())
  }

  requirements {
    container: "python:latest"
  }
}

Example input:

{}

Example output:

{
  "read_object.my_obj": {
    "key_0": "value_0",
    "key_1": "value_1",
    "key_2": "value_2"
  }
}

The command outputs the following lines to stdout:

key_0\tkey_1\tkey_2
value_0\tvalue_1\tvalue_2

Which are read into an Object with the following members: