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Galaxy developers,

I would be particularly interested in seeing this implemented as flow
control blocks. Having such blocks in workflows would vastly expand the
capabilities. Ideally there would be something like

- - for (i=0 to max)
- - foreach (file in files)
- - while
- - if (could pass off "testing" to some external bit of code/another
programme which would return 1/0)
- - switch case

This would allow you to run a copy of the workflow foreach of Jens'
files, and then run another foreach loop on the outputs of the foreach
to concatenate them down to a single file (or something like that to
combine them)

Just my two cents.

Cheers,
Eric

On 12/10/2013 04:05 AM, Preussner, Jens wrote:
> Dear galaxy-dev’s,
> 
>  
> 
> about a year ago you discussed on variable number of inputs into a
> workflow (see
> http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-November/012012.html
> and
> http://thread.gmane.org/gmane.science.biology.galaxy.devel/4502/focus=4502,
> for example). We’re interested in having something simple like a number
> of fastq files that have to undergo automated quality control and
> trimming. A workflow would describe steps that need to be done per file
> (like fastqc, quality trimmer and so on), and in the end, a tabular data
> summarizes statistics on all files. Of course, we could prebuild
> workflows for 2,3,4,5,..n input files and join the output, but it would
> be much cooler to have it variable. Since it’s possible to start many
> instances of a workflow (i.e. one instance per file), this would be a
> good starting point. But how would one combine outputs of those
> instances? Is anyone out there having experience with such setups? Which
> files are involved in starting many instances of a workflow? Any other
> ideas or suggestions on how to go from here? Thanks a lot for any input!
> 
>  
> 
> Best,
> 
> Jens
> 
>  
> 
> Max-Planck-Institute for Heart and Lung Research
> 
> Bioinformatics Service - FGI
> 
> Ludwigstraße 43
> 
> 61231 Bad Nauheim
> 
>  
> 
> Phone. +49 6032 705 1765
> 
> Mail. jens.preuss...@mpi-bn.mpg.de <mailto:jens.preuss...@mpi-bn.mpg.de>
> 
>  
> 
> 
> 
> ___________________________________________________________
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> 

- -- 
Eric Rasche
Programmer II
Center for Phage Technology
Texas A&M University
College Station, TX 77843
404-692-2048
e...@tamu.edu
rasche.e...@yandex.ru
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