Slowly trying to catch up on e-mail after a lot of travel in November
and I answered a variant of this to Damion directly, the most relevant
I would not symbolic link the
files though. I would just take the original collection and pipe it
into the next tool and add a dummy input to the next tool
("passing_qc_text_file") that would cause the workflow to fail if the
qc fails. This is a bit hacky, but symbolic linking will break
Galaxy's deletion, purging, etc.... You can delete the original
dataset collection and the result would affect the files on disk for
the output collection without Galaxy having anyway to know.
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
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"
> At moment we use parameters for format_source="workflow_files"
> metadata_source=“workflow_files” to pass through all the info on an input
> <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" metadata_source="workflow_files” >
> Much obliged!
> 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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