So we loaded the change set that was developed at the hack-a-thon to our instance of galaxy. For the case where I have a directory of input files, where I want to run the same workflow for each, this change works great.
There is one new issue I see, that I'd be interested in input on, and an old issue that I'd like a status on.
First the new... So I have a workflow that does analysis on paired end mRNA Seq data. My workflow for single end works great, but with paired end, I can see an obvious way to submit two lists of files (one for the forward and one for the reverse), which can then be submitted to a series of the same workflow. Once I've chosen the forward to allow selection of multiple input files, the option to allow the reverse to also allow selection of multiple input files becomes disabled. This makes perfect sense, as, unless you've implemented it to associate pairs of files together, this probably wouldn't work anyway. Is there anyone out there working on a solution to this? If not, does anyone have suggestion as to how we could make it work?
Now the old... A while back I suggested that it would be useful while editing a workflow, if there were a way to grab the name of an input file as a variable, and then use this variable in naming all later output files (this way I can propagate a sample name all the way through the workflow). Especially in a case where we are using the option to select multiple files to run the same workflow, this feature is very important. Is anyone working on this? If not, could someone point me in the right direction if I were to start trying to implement this feature?
Thanks,
Dave