Yes, there are options to point to various files. However, it was my understanding that many Pegasus tools permit me to specify the workflow directory as argument, not introduced by any switch, that defaults to the CWD only when none was specified. The Perl equivalent would be something like this:

my $workdir = shift || Cwd::getcwd();

In effect, I would like to see the following behavior:

$ pegasus-analyzer

1. analyzes the current workdir

$ pegasus-analyzer /path/to/workdir

1. analyzes /path/to/workdir work dir