Collaboration

Contributing to AXIOME3 development

You could contribute to AXIOME3 development by providing Python and/or R scripts to analyze or visualize 16S rRNA data.

Please refer to the general coding guideline below

1. Proper error handling

   Raise AXIOME3Error for expected errors

   AXIOME3Error is a custom error that can be found in exceptions/exception.py (you may import it as from exceptions.exception import AXIOME3Error)

2. Your scripts and/or tools are expected to use either QIIME2 outputs (.qza) or QIIME2 derived outputs (exported from .qza files) as inputs.

There are two ways to contribute to AXIOME3 development,

1. Fork AXIOME3 repository and make pull requests (Recommended)

1. Fork AXIOME3 pipeline repository (https://github.com/neufeld/AXIOME3)

2. Try to work with dev branches only (e.g. branches that have "dev" as suffix; "dev", "qiime2-2019.10-dev", etc.)

   • "dev" branch currently uses qiime2-2020.6 version

3. Inside the scripts directory, create a directory with the name of your analysis tool/script, and place your scripts in this directory.

   For example, if you wish to add a script that performs indicator species analysis, you would create a directory called indicator_species_analysis under scripts directory, and place all its associated scripts inside this directory.

4. After making changes, make Pull requests so that repository owner(s) could review the scripts.

2. Send scripts over email (If you are not familiar with using Git)

1. Although not recommended, you may also send scripts to [email protected] with subject "AXIOME3 Collaboration - name_of_your_tool"

2. After reviewing scripts, changes will be merged to AXIOME3.