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.
Modification of Strings
My workflow gets a directory as input which is named like this: [Date][FlowCell][...]_[...]/ To do the mapping with bwa mem I want to extract some of those blocks to use them as part of my readgroup. To do so I use #, ##, % and %% known from shell scripts.
When I validate my wdl script wdltool returns:
Unrecognized token on line 29, column 18:
The # character seems to be the problem. Is it at all possible to work with Strings the way I do it in shell scripts? Is there another way to extract information from strings? I try to avoid packing my wdl script inside of a shell script.