I am pretty confident this worked at some point, this is potentially a regression of some kind (or I am crazy person). I will try to find time to take a closer look. I have created a Trello card for this: https://trello.com/c/9knsbvmx Sorry about that! -John On Wed, Oct 30, 2013 at 12:35 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:

Hi John,

I've just tried a workflow using my MIRA4 de novo wrapper: http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler

To keep it simple, in this example I just had two input FASTQ files, the forward and reverse files for paired end MiSeq data.

This seemed to work fine for re-running the workflow :)

However, on loading the workflow to edit it, only the first input file was drawn linked to the MIRA4 tool. On making some minor workflow changes (renaming some output), and trying to run it, the second input file seemed not to be used.

Is this something you are aware of?

The good news is that I could "re-draw" the missing connection from the second FASTQ file in the workflow editor, and that appears to be working...

Peter

--

This was using the current stable release,

$ hg branch default

$ hg heads changeset: 10421:a477486bf18e branch: stable tag: tip user: Nate Coraor <nate@bx.psu.edu> date: Thu Sep 26 11:02:58 2013 -0400 summary: Bugfix for tool-to-destination mapping, tool ids are lowercased but the mapping id was not lowercased.

changeset: 10411:c42567f43aa7 user: greg date: Mon Aug 19 13:19:56 2013 -0400 summary: Filter invalid objects when generating the list of repository_dependencies objects that are associated with a tool shed repository installed into Galaxy.