Hi, it's a noob question.
I'm practicing cwl with Nucmer software http://mummer.sourceforge.net/manual/#nucmer.
I have described only the help and version argument with :
cwlVersion: v1.0 class: CommandLineTool baseCommand: nucmer inputs: help: type: "null" inputBinding: prefix: -h version: type: "null" inputBinding: prefix: -V outputs: err_msg: type: stderr stderr: output.err
but when running with cwltool ( with help or version arg.) the output.err file only contains :
USAGE: nucmer [options] <Reference> <Query> Try '/home/sletort/logiciels/MUMmer3.23/nucmer -h' for more information.
Is it a wanted behaviour, is my description incomplete ?
=> nucmer outputs help and version on stderr.
... The output is a general output in case of error. So the command line ran is not well formatted.