> Hi,
> I have tried to use tasks with tophat2, but I got the following bug.
> > multi.py +153
> msg = 'nothing to merge for %s (expected %i files)' \
>                           % (output_file_name, len(task_dirs))
> This occurs because tophat2 tool uses from_work_dir feature to get the output 
> files.
> But on the line:
> output_files = [ f for f in output_files if os.path.exists(f) ]
> It returnes an empty list because no real output files exists.

Tophat2 cannot be parallelized because it uses a shared junctions database, and 
shared objects are not yet supported by Galaxy's parallelism.

That said, it's likely the case that parallelism + from_work_dir do not work 
together yet; I've created a card for this issue: https://trello.com/c/5fFZSCWn


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