We've moved!
For WDL questions, see the WDL specification and WDL docs.
For Cromwell questions, see the Cromwell docs and please post any issues on Github.

Using variables that are result of unix commands

Hi! I have a task where I am naming the file according to the first line in the file i.e. the result of the command "head -1 FILENAME". I successfully passed it to my command line, but I cannot grab the file with the output:

task suppa_psi {

  File gtf
  File abund

  command {
    suppa.py psiPerIsoform -g ${gtf} -e ${abund} -o $(head -1 ${abund})

  output {
    File psi_file = "$(head -1 ${abund})_isoform.psi"

  runtime {

The output filename is interpreted literally, which I suppose happens because there is no shell to perform the expression.
I also tried creating a new variable in the definitions "String name = head -1 ${abund}" or "String name = $(head -1 ${abund})" and neither was parsed properly.
How can I grab this file?

Sign In or Register to comment.