RSEM prepare reference tool does not produce valid reference files

Hello, I’m doing some differential expression analysis on RNA-Seq data. All steps have been previously (successfully) run in command line and now I’m trying to create a workflow on Galaxy for the same procedure.

I got stuck on using the RSEM tool. When I try to run RSEM prepare reference, it does not produce the “red error”, but it does not produce a valid RSEM reference file either. When I try to use the created reference file in the next step, the RSEM calculate expression, the tool does not recognise any valid reference files in my history. I downloaded and inspected the file and it contains only the name of the file in it and nothing else.

When using RSEM prepare reference, I have tried creating the reference in 3 different ways, using the:

  1. previously assembled transcriptome
  2. newly assembled transcriptome that I have assembled on Galaxy
  3. reference genome and a gtf file
    and none of it creates the “red error” or the valid file.

When I do it independently of Galaxy in command line with the same data, it all works fine so it doesn’t seem like the problem lies in the data. Can someone please tell me if I’m doing something wrong or there’s a bug in the tool?

Thank you!