Yes, there is a relationship - in the database there's also a 
WorkflowStepConnection table that relates inputs and outputs (WorkflowStep + 
i/o name) between steps.

On Dec 28, 2012, at 8:33 AM, Sachit Adhikari <sachit.techner...@gmail.com> 
wrote:

> Hi Dannon,
> 
> Thank you for your answer. What I meant by the last question is that:
> 
> When I create a workflow (tophat-bowtie-bowtie2). The input is first 
> processed by tophat and the output of tophat is processed by bowtie and then 
> the output of bowtie and processed by bowtie2 and that's the final output. 
> There's some sort of relationship, right? Is this relationship stored in 
> database? 
> 
> On Fri, Dec 28, 2012 at 7:34 AM, Dannon Baker <dannonba...@me.com> wrote:
> A workflow is just the definition of a particular process or set of steps.  
> This information is stored in the database (see Workflow, StoredWorkflow, 
> WorkflowStep tables).  Running that workflow creates datasets in a history 
> (datasets which are stored in database/files).
> 
> And, I'm not sure exactly what you're asking in your last question, can you 
> clarify?
> 
> -Dannon
> 
> 
> On Dec 28, 2012, at 2:16 AM, Sachit Adhikari <sachit.techner...@gmail.com> 
> wrote:
> 
> > I have searched the mailing list and found that the output, histories and 
> > workflows are stored in ~/database/files. To do a little experiment I 
> > deleted all the inside that directory. I then open my Galaxy and browse the 
> > workflow. But the workflow is still there. I was wondering where is the 
> > workflow stored in Galaxy? Also, if possible can I know how is the 
> > relationship specified by user while creating workflow is stored?
> >
> > Happy New year
> >
> > Regards,
> >
> > Sachit
> > ___________________________________________________________
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> 

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