mkdocs.yaml

# Project Information
site_name: SF_biocontainer Documentation
site_author: CCRSFIFX
site_description: >-
  SF_biocontainer is a github repo with the Dockerfile used to build containers for CCRSF pipelines.  

# Repository
repo_name: CCRSF-IFX/SF_biocontainer
repo_url: https://github.com/CCRSF-IFX/SF_biocontainer.git 
edit_uri: https://github.com/CCRSF-IFX/SF_biocontainer/edit/main/docs/

# Copyright
copyright: Copyright © 2024 CCRSFIFX

theme:
  name: readthedocs
  highlightjs: true
  hljs_languages:
    - yaml
    - rust

# Customization
extra:
  social:
    - icon: fontawesome/brands/github
      link: https://github.com/CCRSF-IFX

# Page Tree
nav:
  - Intronduction:
      - Containerization: index.md
      - Create image/container: docker.md
      
  - Containerization for Snakemake pipeline:
      - Build Snakemake pipeline with Singularity: pipeline_containerization.md
      - Snakemake options for containerization: snakemake_opt4singularity.md 
      - Develop R scripts in the container: dev_w_docker.md
      - Run command lines using the container outside snakemake pipeline using Singularity: exec_cmd_sif.md 
  - FAQ:
      - General Questions: general-questions.md
      - Troubleshooting: troubleshooting.md
  - Reference: ref.md
  - License: license.md