Thon,

Not currently, though the question comes up often enough that I'll try and bump 
it up my list.  

Instead of interlacing and deinterlacing a better workaround for now might be 
to use the API to execute over all these samples.

-Dannon

On Feb 13, 2012, at 8:46 PM, Anthonius deBoer wrote:

> 
> Hi,
> 
> Is there an intelligent way to run a workflow that starts with more than one 
> pair of paired-end data sets in a workflow?
> I can run multiple workflows when there is a SINGLE input file, but in the 
> case of many paired end workflows, you need to provide two paired samples and 
> just adding another input workflow step does not work, since you can only 
> select a single file in the second input workflow set.
> 
> I realize that there is an issue with the cycling through the datasets since 
> they need to be paired-up and it would be very easy to mess this up if you 
> allow two (or more) input data sets, but since paired end data is going to be 
> very common, I would assume a special paired end input workflow step that is 
> intelligent and can pair up the input datasets before handing them off to the 
> workflow would be very useful.
> 
> I can think of workarounds ofcourse, such as creating an interlaced file 
> containing both pairs and then just de-interlacing them in the workflow, but 
> that is kludgy and will result in a lot of data duplication for no reason...
> 
> I have to run 88 samples which will soon grow to over 200 samples, so running 
> each step manually is not really an option and I would hate to have to 
> program the workflow steps myself...
> 
> Any ideas?
> 
> Thanks
> 
> Thon
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