Hi Stian, thanks for the reply. Yes, it is only for analytical purposes, trying to understand if modularisation suggestions can be made.
thanks again pinar > In the Taverna workbench you can insert a nested workflow by merging. > You can merge in any workflow, including workflows open in the > workbench. > > To merge in an existing nested workflow, first Right-click on it to > Edit Nested Workflow. > > Now go back to the original workflow using the Workflows menu, where > you click in the top menu Insert -> Merge workflow. > > In the dialogue, select Workflow Source: Already opened workflow - > and select "XXXX in YYY" - the newly opened nested workflow. > > Now you will have to rewire each step of the nested workflow. There > will be new input ports added to your workflow, which one by one you > will have to: Delete the new input port (otherwise the next step will > add a merge), then find the corresponding datalink that goes into the > old nested workflow, and click to drag it into the processor(s) that > the just-deleted input port just to go to. > > Repeat for nested workflow output ports. You would in this case first > need to delete the existing outgoing datalinks from the nested > workflow to avoid making merges into the processors of the master > workflow. > > Finally you can close and delete the old nested workflow and repeat > the processor for the remaining (including any previously nested > nested) workflows. > > > > Note that the execution logic totally changes by merging in a nested > workflow, and the resulting workflow is unlikely to produce the same > results for common uses of nested workflows. > > > For instance, if there are iterations over the nested workflow, now > you would have iterations over the immediate first processors instead > (and their downstreams) - which might in some cases require you to > reconfigure List Handling on every step of the workflow. > > Many nested workflows are used with iterations both inside and outside > the nested workflows - in which case there are several List Handling > iteration patterns which can't easily be expressed on a merged > workflow, say outer Dot product and inner Cross product. > > > A nested workflow executes in 'one go' - so the next steps consuming > its outputs don't execute before everything in the nested workflow has > finished (including 'dangling processors' without outputs, typically > used for clean-up). Similarly it does not start until all the inputs > are present. After merging, Taverna's pipelined execution means that > the individual steps will now be detangled and execute as soon as data > is available -- this might be what you want if the nested workflow > unnecessarily caused a slow-down of parts of its processes. You can > add Run After links to try to coordinate some of these, but even this > would give a different execution logic as it would require the full > outer iterations to have completed. > > > Any processor-level configuration on a nested workflow would also > disappear, e.g. List Handling, Looping and Parallel Jobs. So any > workflows doing asynchronous services such as the EBI InterproScan > would not work. > > > > tl;dr; In many cases, execution will NOT be the same after flattening. > > > So I am left to wonder what is the reason for your flattening.. it can > make sense in some cases - but more often than not it doesn't - which > is why we have not got such as feature built in to the workbench. > > Are you doing this for the purpose of executing the flattened > workflows, or just for analytical purposes? > > > On 17 November 2013 20:44, Pinar Alper <[email protected]> wrote: >> >> >> Hi all, >> >> For an evaluation that I'm performing I need flattened versions of >> workflows with sub-workflows in them. >> >> I was just wondering if there is an easy way to unnest a sub workflow in >> Taverna. Or should I copy all sub-processors one by one to the parent >> workflow? >> >> >> -- >> regards >> pinar >> >> ------------------------------------------------------------------------------ >> DreamFactory - Open Source REST & JSON Services for HTML5 & Native Apps >> OAuth, Users, Roles, SQL, NoSQL, BLOB Storage and External API Access >> Free app hosting. Or install the open source package on any LAMP server. >> Sign up and see examples for AngularJS, jQuery, Sencha Touch and Native! >> http://pubads.g.doubleclick.net/gampad/clk?id=63469471&iu=/4140/ostg.clktrk >> _______________________________________________ >> taverna-users mailing list >> [email protected] >> [email protected] >> Web site: http://www.taverna.org.uk >> Mailing lists: http://www.taverna.org.uk/about/contact-us/ > > > > -- > Stian Soiland-Reyes, myGrid team > School of Computer Science > The University of Manchester > http://soiland-reyes.com/stian/work/ http://orcid.org/0000-0001-9842-9718 > -- regards pinar ------------------------------------------------------------------------------ Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. 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