xpresspipe riboseq UMI bug?

XPRESSyourself / XPRESSpipe

An alignment and analysis pipeline for Ribosome Profiling and RNA-seq data

https://xpresspipe.readthedocs.io/en/latest/

GNU General Public License v3.0

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xpresspipe riboseq UMI bug? #38

Closed hollyjaro closed 4 years ago

hollyjaro commented 4 years ago

Hello,

I am trying to run the xpresspipe riboseq but I am getting the same error, I believe it's from the fastp package for UMI:

TypeError: can only concatenate str (not "int") to str

I tried to play with the --umi_location (read2, "read2", =read2) and --umi_length 5 with I am getting the same error. I am not very skilled in bioinformatics. Please see attached the log file. ribo_pipe.txt

j-berg commented 4 years ago

Hi,

I'm so sorry for the delay in getting back to you. For some reason, issues aren't getting sent to my email as I expected. I am working on fixing this so I can be more prompt in responding!

I think I tracked down the bug you mentioned. If you re-install XPRESSpipe using this version, it should address the issue you are running into.

Please don't hesitate to reach out to me if you have more questions!

Jordan

j-berg commented 4 years ago

Closing issue. Please re-open if you have any issues with the update or need help. Thanks!