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}])
write(mapped,
ofile=ARGV[2])
The resulting tool will take two arguments, specifying its input and output.