WDL Parser

This repo contains code used to publish pip packages for the parsers located in the official WDL repository. Using those packages, you can parse WDL workflows under any version of the WDL specification.

Installation

To install the parsers, run:

pip install wdl-parser

Usage

Direct Import

The WDL parsers are provided within one package named wdl_parser. One module exists inside this for each version of the spec, with all hyphens and dots replaced by underscores. Thus, the modules available to import are:

• wdl_parser.version_1_0
• wdl_parser.development
• wdl_parser.draft_2
• wdl_parser.draft_3

Each of these modules exposes a parse function, which takes a string containing the WDL to parse. For example:

from wdl_parser import draft_2

with open('./gatk4-data-processing/processing-for-variant-discovery-gatk4.wdl') as wdlfile:
    tree = draft_2.parse(wdlfile.read())

Parser Dictionary

Alternatively, if you want to access a parser based on its official name, you can import the base module, and access the parser dictionary like this:

import wdl_parser

with open('./gatk4-data-processing/processing-for-variant-discovery-gatk4.wdl') as wdlfile:
    tree = wdl_parser.parsers['draft-2'].parse(wdlfile.read())

Operating on the AST

Once you have the AST, refer to the Hermes documentation for more information on how to use it.