Skip to content
Branch: master
Find file Copy path
Find file Copy path
Fetching contributors…
Cannot retrieve contributors at this time
30 lines (17 sloc) 755 Bytes

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 "0.8"

mapped = samfile(ARGV[1])

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


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

You can’t perform that action at this time.