Wrapping a script which implicitly expects a local file

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@sdunc in this case, we would normally symlink the files at the start of the command. If the steps are running as part of the same script, you can always mkdir and mv files as they are generated in the working directory.

ex.

mkdir new_dir &&
ln -s $input_1_varname new_dir/prefix_I_want.ext &&
ln -s $input_2_varname new_dir/prefix_I_want.ext2 &&
EmmaScript -t new_dir/<prefix>
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