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Prior to EAGLE-121, the command line for a BashShellApp was specified using a set of parameters beginning with Arg. For example:
However, this caused issues when attempting to determine which arguments specified the command itself, the input redirection and the output redirection.
Some workflow systems (for example CWL) require these parts to be specified separately.
EAGLE-121 introduced default parameters in the BashShellApp for each part of the command line. This change to DALiuGE supports that change. The contents of additional named parameters is added to the final command line.
I've left the existing method (using Arg01, Arg02, etc) in the code. Since it is likely that only one of the two methods would be used. We have a large number of graphs that use the old method.