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
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.
On Sun, Nov 1, 2015 at 8:12 PM, Dooley, Damion <Damion.Dooley(a)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"
> At moment we use parameters for format_source="workflow_files"
metadata_source=“workflow_files” to pass through all the info on an input dataset...
> <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'." />
> <data name="workflow_files_pass"
format_source="workflow_files" label="Workflow datasets"
> Much obliged!
> Hsiao lab, BC Public Health Microbiology & Reference Laboratory, BC Centre for
> 655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 Canada
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