How do I force Cromwell / WDL to put input files in the same directory?
My hacktastic fix for this is to use basename to get the get the name of each file, then do
refName=`basename &quot;${Ref}&quot;`
ln -s &quot;${Ref}" "$refName&quot;

for each file.  This puts aliases to each file in the executions dir, and then I pass &quot;refName&quot; to GATK rather than &quot;${Ref}&quot;.
Not a good solution, but a solution