Options to edit parameters of each tool

[irvinng98]

Hello,

Given that each tool used in the pipeline has multiple options/flags, I was wondering if there is a place where I can specify certain parameters other than the few lines in the config.ini file.

Im running into an issue of my reads not getting merged

Vsearch Merge pairs
vsearch v2.7.1_linux_x86_64, 187.5GB RAM, 16 cores
https://github.com/torognes/vsearch

Merging reads 100%  
  63708703  Pairs
     24311  Merged (0.0%)
  63684392  Not merged (100.0%)

Pairs that failed merging due to various reasons:
  14256882  too few kmers found on same diagonal
     57798  potential tandem repeat
        89  too many differences
  49121432  alignment score too low, or score drop to high
    248191  staggered read pairs

and I would like to try some changes in the parameters of VSEARCH. Please advise. Thanks!

[billytaj]

not yet, but that's not a bad idea.
I'll open up all of the options in the next version.
However, due to org design, the config settings will stay contained in the config file.

Thanks for the suggestion!

In the meantime, you're free to tweak your commands manually.
Try using docker/singularity in shell-mode and go from there.