Common Workflow Language Integrations

Simple operations

Simple NGLess operations can be performed through the command line wrappers, all of which have a CWL tool description.

Automatic CWL export of NGLess scripts

An NGLess script that conforms to certain rules can be exported as a CWL tool using the --export-cwl option:

ngless script.ngl --export-cwl=tool.cwl

The rules are simple: the script must use ARGV for its inputs and outputs. For example, this is a conforming script:

ngless "0.0"

mapped = samfile(ARGV[1])

mapped = select(mapped, drop_if=[{mapped}])

write(mapped,
        ofile=ARGV[2])

The resulting tool will take two arguments, specifying its input and output.