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wdl with optional flags
I have a command in my workflow that accepts an optional flag, like this:
command.py --input infile --ouput outfile --flag
I would like to include
flag in the workflow as a boolean variable, and have
command.py called as above when it is true, and like this when its false:
command.py --input infile --ouput outfile
Is there a way to do this within the 'command' block? I could make a separate task for the command with and without the flag, but this won't work if we want to include many different optional flags.
For reference, I have found a way to use
command.py with optional
--val=foobar, but I see no clear way to modify that method for flags without values: http://gatkforums.broadinstitute.org/wdl/discussion/7024/optional-parameters-and-type-constraints