DEV-1486 Make CRAM output off by default

hartwigmedical / platinum

Run multiple Pipeline5 instances at once

GNU General Public License v3.0

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DEV-1486 Make CRAM output off by default #12

Closed nedleitch closed 4 years ago

nedleitch commented 4 years ago

Also rework the arguments ordering so that only those we want to allow to, can be overridden. We are dependent on the argument parsing code in Pv5 which currently honours the first-specified instance for arguments with multiple instances on the command line.