On 11/17/2015 01:18 PM, John Chilton wrote:
> The workflow subsystem has the ability to define a connection like
> this (just wait for one tool to pass before calling the next without a
> input/output relationship) but it hasn't been exposed in the workflow
> editor yet.
That's incredibly exciting John. Can't wait for workflow availability of that 
feature. It was a huge problem for my tools when I was writing internal 
wrappers which did ordering dependent operations on external databases. Good to 
hear it's going to be possible.
> -John
>
>
> On Sun, Nov 1, 2015 at 8:12 PM, Dooley, Damion <damion.doo...@bccdc.ca> wrote:
> > Has anyone done a tool part of which simply takes in a data collection and 
> > provides it (symlinked) in a corresponding output data collection?  We have 
> > a quality control tool that enables us to stop workflow, preventing 
> > subsequent jobs to be run if a problem has been detected.  Currently our 
> > tool only sym-links through an individual dataset.  It would be great if it 
> > could work on a whole data collection of any sort.
> >
> > I see there’s a <collections> tag now – is there an easy solution using 
> > this – and that doesn’t loose metadata?
> >
> > <collection name=“genericCollectionSymlink" label=“Workflow datasets”>
> >    <discover_datasets pattern=???????????? visible="true"  
> > ......................?????????
> > </collection>
> >
> > At moment we use parameters for format_source="workflow_files" 
> > metadata_source=“workflow_files” to pass through all the info on an input 
> > dataset...
> >
> > <inputs>
> >    …
> >    <param name="workflow_files" type="data" optional="True" 
> > multiple=“False" label="Workflow data" help="Select dataset(s) that 
> > subsequent workflow stages can consume if report status is not fail'." />
> > </inputs>
> > <outputs>
> >    <data name="workflow_files_pass" format_source="workflow_files" 
> > label="Workflow datasets"  metadata_source="workflow_files” >
> >       <filter>(workflow_files)</filter>
> >    </data>
> > </outputs>
> >
> >
> > Much obliged!
> >
> >
> > Damion
> >
> >
> > Hsiao lab, BC Public Health Microbiology & Reference Laboratory, BC Centre 
> > for Disease Control
> > 655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 Canada
> > ___________________________________________________________
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-- 
Eric Rasche
Programmer II

Center for Phage Technology
Rm 312A, BioBio
Texas A&M University
College Station, TX 77843
404-692-2048
e...@tamu.edu

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