Question about parameter in workflow about bioblend

[nsoranzo]

I think it should be:

params = {
    'bowtie2': {
        'reference_genome': {
            'source': 'indexed',
            'index': 'hg19'
        }
    }
}

This will affect all steps having 'bowtie2' as tool id.
To modify only a specific bowtie2 step, you can just substitute 'bowtie2' with the step id, which is also the recommended syntax.

[nsoranzo]

@LongTianPy: do my suggestions work for you? If yes, I'd like to improve the method documentation.

[LongTianPy]

@nsoranzo Hi, sorry I missed your previous reply. I have solved my problem in another approach but haven't tried your suggestions. My question about your suggestions is when I'm trying to figure out the parameter, should I go to the tool's XML wrapper to find out the keys of the dictionary?

[nsoranzo]

@LongTianPy: Looking at the XML is one option, the other is:

w = gi.workflows.show_workflow('<workflow_id>')
step = [_ for _ in w['steps'].itervalues() if _['tool_id'] == '<tool_id>'][0]
print step['tool_inputs']

but this will give you the parameters only for the current selection of <conditional>s.

[LongTianPy]

@nsoranzo Thanks, this really helped me.

[nsoranzo]

Documentation has been improved in d3911bf, thanks for your question!