I'm trying to run a simple WDL that runs "samtools mpileup", where one WDL parameter is the name of an intervals file. From FireCloud I enter the intervals filename as follows
" gs://fc-ca79cf19-a640-44f1-beed-751b14874ad2/misc_files/testing.intervals"
This testing.intervals is a simple text file that I uploaded to the google bucket using gsutil. I know the file exists at that location because a "gsutil cp gs://fc-ca79cf19-a640-44f1-beed-751b14874ad2/misc_files/testing.intervals ." command works fine.
However when I run my WDL (in the same google bucket), I get the following error
samtools mpileup: Could not read file "gs://fc-ca79cf19-a640-44f1-beed-751b14874ad2/misc_files/testing.intervals": No such file or directory
Any advice?