This section of the forum is now closed; we are working on a new support model for WDL that we will share here shortly. For Cromwell-specific issues, see the Cromwell docs and post questions on Github.
Plink prefix and wdl
I am trying to create a WDL that runs plink and takes as an input a prefix to the bed/bim/fam file
I am using Cromwell and docker to run it
plink -bfile prefix --recode --out prefix
Cromwell copies over the input files. How do I configure the wdl to use a prefix and grab the files associated with the prefix without explicitly defining the files. Also even if I can get the files copied over how do I pass a prefix to the files?