Ah, I can see how symlinking could lead to file management issues. Well,
we were trying to avoid the situation where use of our qc tool would
require customizing any subsequent tools in a workflow, and as well,
reduce disk overhead of hundred megabyte files being passed along in a
So wow on the second paragraph - enabling dependencies outside of tool
file I/o. I agree with Eric, this will be great.
Now in our current canned workflows we actually don't need this to be
edited via the interface - so are there details on how to edit a workflow
file directly to get this dependency of tool B on tool A in place?
On 2015-11-17, 11:18 AM, "John Chilton" <jmchilton(a)gmail.com> wrote:
Slowly trying to catch up on e-mail after a lot of travel in
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