I wrote a simple WDL workflow to run Picard's MergeSamFiles on a group of BAM files. The execution repeatedly fails with the same error. The script is attached as merge_script.txt.
The logfile indicates that the URLs for the input files can't be accessed. The logfile is attached as merge_log.txtI verified that the URLs exist by running gsutil ls from my local terminal on the exact URLs. The input BAM files are in my account's google cloud bucket and were generated from another workflow in my account, so it wouldn't seem to be a permissions issue.
I can share my workflow if that's helpful; I didn't want to clutter this up any more than I already am. Basically it's using read_lines to pull a list of gs:// URLs from a text file. It's clearly doing that part correctly based on the generated script.
Suggestions/speculations in lieu of answers are very welcome--I'm happy to do the legwork.
Thanks!