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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