To celebrate the release of GATK 4.0, we are giving away free credits for running the GATK4 Best Practices pipelines in FireCloud, our secure online analysis portal. It’s first come first serve, so sign up now to claim your free credits worth $250. Sponsored by Google Cloud. Learn more at https://software.broadinstitute.org/firecloud/documentation/freecredits

Accessing BASH internal variables

Hi,

Bash has an internal variable called ${PIPESTATUS} which stores the exit code of each command in the pipeline. I was trying to use this in my wdl code to capture individual exit codes in the pipeline.

test ${PIPESTATUS[0]} -eq 0

The error :

ERROR: Variable PIPESTATUS does not reference any declaration in the task (line 39, col 14):

      test ${PIPESTATUS[0]} -eq 0
             ^

Task defined here (line 16, col 6):

task BWA_Mem {

When I try to validate my code I receive an error. May I know if there is a work around to access internal bash variables in wdl?

Tagged:

Best Answer

Answers

Sign In or Register to comment.