mkdocs.yml

site_name: "Kew Bioinformatics Documentation"
site_url: https://rbg-kew-bioinformatics-utils.readthedocs.io

theme: 
  name: readthedocs
  highlightjs: true

plugins: 
  - search
  - mkdocstrings:
      handelers:
        python:
          option:docstring_style: sphinx
markdown evtentions:
  - markdown_include.include:
      base_path: .
  - admonition


nav: 
  - KewHPC:
    - System Description: KewHPC/Overview.md
    - Getting Connected: KewHPC/Logging_in_via_ssh.md
    - Transfering Files: KewHPC/Transfer_data_via_sftp.md
    - Data Storage: KewHPC/Where_to_store_data.md
    - Running Jobs: KewHPC/Running_Analysis_with_SLURM.md
    - Using Software: KewHPC/Using_Software_with_LMOD.md
#    - Environment Management and Containers: conda_singularity.md
  - Other Services:
    - Remote Access: Other_Services/remote_access.md
    - Sharing Data : Other_Services/External_SFTP_Service.md
  - Tutorials:
    - Anaconda: software/anaconda.md
#    - BASH (Linux Command Line): software/bash.md
    - GATK: software/gatk.md
    - HybPiper: software/hybpiper.md
    - Ipyrad: software/ipyrad.md
    - Python: software/python.md
    - R: software/r.md
    - Trimmomatic: software/trimmomatic.md