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.preussner@mpi-bn.mpg.de