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Oshlack / JAFFA

JAFFA is a multi-step pipeline that takes either raw RNA-Seq reads, or pre-assembled transcripts, then searches for gene fusions
https://github.com/Oshlack/JAFFA/wiki
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Error when output directory specified #68

Closed shernadi closed 2 years ago

shernadi commented 2 years ago

Hi,

I am experiencing some issues when I try to run JAFFAL with specifying an output directory (both when using bpipe -d or -p jaffa_output="" . It seems the pipeline fails when it try to generate the final output files. I am also wondering if there is an easy way to exclude the input file prefix from the output directory? 

Compiling the results from:
read.test
Error in file(file, "rt") : invalid 'description' argument
Calls: read.delim -> read.table -> file
Execution halted
ERROR: stage compile_all_results failed: Command in stage compile_all_results failed with exit status = 1 :
nadiadavidson commented 2 years ago

Thanks for bringing this to my attention. I'll look into a bug fix for this in the next release.

As a work around you can get JAFFAL to output into any directory:

  1. Create and change into the directory where you want the output: mkdir MyOutputDir cd MyOutputDir
  2. Run JAFFAL as normal (without the -p jaffa_output="". It will default to the current directory).

The input file prefixes can't easily be removed from the output directories and names.

Please let me know if you have any further problem or questions.

nadiadavidson commented 2 years ago

Fixed in commit 6bcad6ae3f0d8d258fcb7954705ef0c3c3eeddb6 Along with #72 #70