Okay, so I'm caught up on my Galaxy Dev reading, and now realize that the thread on calling workflows programmatically is discussing what I need to do. I would still be curious to know if something is planned for the Galaxy workflow interface, that would allow you go configure a workflow to take multiple inputs, run the workflow for each of these inputs, and then allow me to pass the end result of the workflows to a single "merging" or "aggregating" tool. However, in the meantime, I'm going to try the api interface to workflows and see if that means my near term needs. Thanks, Dave On 3/18/11 11:23 AM, "Dave Walton" <dave.walton@jax.org> wrote:

I'm curious if there is a way to create a workflow as follows (or if anyone else thinks this is a good idea, or for that matter has a good suggestion of another solution):

1) User selects N groomed fastq files and puts them in a history

2) User selects a workflow that allows them to select the N files, and then passes each of them to a two step process that first runs them through tophat, and the resulting bam file through cufflinks.

3) At the other end of the workflow would be a merge module that would take one of the 3 output files from cufflinks from each run, and does some sort of aggregation or transformation step on all the resulting data.

Any input would be greatly appreciated.

Thanks,

Dave

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