otb.sh is a nextflow pipeline for generating hifiasm assemblies usually utilizing hicstuff. The primary benefit of otb is that it can standardize assembly runs, likely if you’ve hit this contributions page you are here for one of two reasons:
1.) You wither wish too or have implemented otb in you’re your own organization and you wish to submit bug fixes and documentation upstream for the benefit of others. 2.) You wish to expand the capabilities of otb or introduce alternative tooling into the pipeline
Eitherway, thank you. We’re glad to have you. We ask that you follow a general development workflow of creating a fork and pull request, we ask that: You mention the issue you are trying to address in the pull reqquest, be specific as possible, also always write a clear log message for your commits. One-line messages are fine for small changes, but bigger changes should look like this:
$ git commit -m "A brief summary of the commit
>
> A paragraph describing what changed and its impact."
In addition we use two space soft tabs and have actions setup to detect whitespace after lines of code.
Please checkout: otb.sh flags