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mkdocs.yml
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# Project information
site_name: 'Bioinformatics Workshop on Tools for Reproducible Research'
site_author: 'Jacques Dainat et al.'
site_url: 'https://southgreenplatform.github.io/training_reproducible_research/'
site_description: Workshop on Tools for Reproducible Research
site_dir: public # When you build your site, all of the files are written to the directory assigned to the site_dir configuration option (defaults to "site")
# Repository
repo_name: 'training_reproducible_research'
repo_url: 'https://github.com/SouthGreenPlatform/training_reproducible_research'
edit_uri: edit/main/docs/ # Allow to replace edit/master/docs use by default
# Configuration
theme:
name: material
logo: pages/images/southgreen.png # logo top left page
search_index_only: true
include_search_page: true
features:
- announce.dismiss
- content.action.edit
- content.action.view
- content.code.annotate
- content.code.copy
# - content.tabs.link
- content.tooltips
- header.autohide
# - navigation.expand
- navigation.footer
- navigation.indexes
# - navigation.instant
# - navigation.prune
# - navigation.sections # collapse subsections
- navigation.tabs
# - navigation.tabs.sticky
- navigation.top
- navigation.tracking
- search.highlight
- search.share
- search.suggest
- toc.follow
- toc.integrate # remove table of content on the right side
palette:
- scheme: default
primary: indigo
accent: indigo
toggle:
icon: material/brightness-7
name: Switch to dark mode
- scheme: slate
primary: indigo
accent: indigo
toggle:
icon: material/brightness-4
name: Switch to light mode
extra_css:
- stylesheets/extra.css
# Extensions
markdown_extensions:
- admonition
- attr_list
- md_in_html
- pymdownx.details
- pymdownx.superfences
- pymdownx.tabbed
- pymdownx.snippets:
base_path: docs
- pymdownx.emoji:
emoji_index: !!python/name:materialx.emoji.twemoji
emoji_generator: !!python/name:materialx.emoji.to_svg
- tables
- toc:
permalink: '#'
# Plugins
plugins:
- search:
separator: '[\s\-,:!=\[\]()"`/]+|\.(?!\d)|&[lg]t;|(?!\b)(?=[A-Z][a-z])'
- minify:
minify_html: true
- external-markdown
- table-reader
- macros
# Customization
extra:
# homepage: # Page displayed when clicking the logo
history_buttons: false
# --- set whole scope variables ---
contact: https://www.southgreen.fr/contact
institute: SouthGreen
color_table_header: "#333a99"
training_path: "~/training-reproducible-research-area"
# page tree
nav:
- Home: index.md
- Tutorials:
- Introduction: pages/introduction/introduction_southgreen.md
- Roundtable Introduce Yourself: pages/introduction/roundtable.md
- Introduction Reproducible Research: pages/introduction/introduction_rr.md
- Data Management: pages/data-management/data-management.md
- Ice breaker session: pages/ice-breaker.md
- Git:
- Introduction: pages/git/git-1-introduction.md
- Setup: pages/git/git-setup.md
- Creating a git repository: pages/git/git-2-creating-repositories.md
- Committing changes: pages/git/git-3-committing-changes.md
- Undoing and recovering: pages/git/git-undoing-and-recovering.md
- Ignoring files: pages/git/git-4-ignoring-files.md
- Branching and merging: pages/git/git-5-branches.md
- Tagging commits: pages/git/git-6-tags.md
- Working remotly: pages/git/git-7-working-remotely.md
- Conflict: pages/git/git-8-conflicts.md
- Extra material: pages/git/git-9-extra-material.md
- Conda:
- Introduction: pages/conda/conda-1-introduction.md
- Setup: pages/conda/conda-installation.md
- The basics: pages/conda/conda-2-the-basics.md
- Projects: pages/conda/conda-3-projects.md
- Extra material: pages/conda/conda-4-extra-material.md
- Workflow Manager System:
- Introduction: pages/wms.md
- Snakemake:
- Introduction: pages/snakemake/snakemake-1-introduction.md
- Setup: pages/snakemake/snakemake-installation.md
- The basics: pages/snakemake/snakemake-2-the-basics.md
- Visualising workflow: pages/snakemake/snakemake-3-visualising-workflows.md
- The MRSA Workflow: pages/snakemake/snakemake-4-the-mrsa-workflow.md
- Parameters: pages/snakemake/snakemake-5-parameters.md
- Logs: pages/snakemake/snakemake-6-logs.md
- Temporary files: pages/snakemake/snakemake-7-temporary-files.md
- Targets: pages/snakemake/snakemake-8-targets.md
- Shadow rules: pages/snakemake/snakemake-9-shadow-rules.md
- Generalizing workflows: pages/snakemake/snakemake-10-generalizing-workflows.md
- Extra material: pages/snakemake/snakemake-11-extra-material.md
- Nextflow:
- Introduction: pages/nextflow/nextflow-1-introduction.md
- Setup: pages/nextflow/nextflow-installation.md
- Getting started with nf-core: pages/nextflow/nextflow-nfcore.md
- The basics: pages/nextflow/nextflow-2-the-basics.md
- Executing workflows: pages/nextflow/nextflow-3-executing-workflows.md
- Working with process: pages/nextflow/nextflow-4-working-with-processes.md
- Workflow configuration: pages/nextflow/nextflow-5-workflow-configuration.md
- Optmising the MRSA workflow: pages/nextflow/nextflow-6-optimising-the-mrsa-workflow.md
- Extra material: pages/nextflow/nextflow-7-extra-material.md
- Containers:
- Introduction: pages/containers/containers-1-introduction.md
- Setup: pages/containers/containers-installation.md
- The basics: pages/containers/containers-2-the-basics.md
- Building a Docker image: pages/containers/containers-3-building-images.md
- Managing containers: pages/containers/containers-4-managing-containers.md
- Distributing your images: pages/containers/containers-5-sharing-images.md
- Packaging the case study: pages/containers/containers-6-packaging-the-case-study.md
- Singularity: pages/containers/containers-7-singularity.md
- Extra material: pages/containers/containers-8-extra-material.md
- Notebook:
- Context: pages/notebook/notebook-context.md
- Markdown: pages/notebook/notebook-markdown.md
- R Markdown:
- Introduction: pages/rmarkdown/r-markdown-1-introduction.md
- Setup: pages/rmarkdown/r-markdown-installation.md
- The basics: pages/rmarkdown/r-markdown-2-the-basics.md
- Text: pages/rmarkdown/r-markdown-3-text.md
- Code chunks: pages/rmarkdown/r-markdown-4-code-chunks.md
- The YAML header: pages/rmarkdown/r-markdown-5-the-yaml-header.md
- Rendering: pages/rmarkdown/r-markdown-6-rendering.md
- The MRSA case study: pages/rmarkdown/r-markdown-7-the-mrsa-case-study.md
- Extra materiel: pages/rmarkdown/r-markdown-8-extra-material.md
- Jupyter:
- Introduction: pages/jupyter/jupyter-1-introduction.md
- Setup: pages/jupyter/jupyter-installation.md
- The basics: pages/jupyter/jupyter-2-the-basics.md
- Magics: pages/jupyter/jupyter-3-magics.md
- Plotting: pages/jupyter/jupyter-4-plotting.md
- Widgets: pages/jupyter/jupyter-5-widgets.md
- Extensions: pages/jupyter/jupyter-6-extensions.md
- Converting notebooks: pages/jupyter/jupyter-7-converting-notebooks.md
- The MRSA case study: pages/jupyter/jupyter-8-the-mrsa-case-study.md
- Extra material: pages/jupyter/jupyter-9-extra-material.md
- Quarto:
- Introduction: pages/quarto/quarto-1-introduction.md
- Setup: pages/quarto/quarto-installation.md
- The basics: pages/quarto/quarto-2-the-basics.md
- Rendering: pages/quarto/quarto-3-the-rendering.md
- Extensions: pages/quarto/quarto-4-the-extensions.md
- The MRSA case study: pages/quarto/quarto-5-the-mrsa-case-study.md
- Comparison: pages/quarto/quarto-6-comparison.md
- Extra material: pages/quarto/quarto-7-extra-material.md
- 'Making a project reproducible':
- Review: pages/project/project-1-review.md
- Good praticies: pages/project/project-2-good_praticies.md
- And now ?: pages/project/project-3-and_now.md
- To end on a high note !: pages/project/project-4-demo.md
- 'Take down': 'pages/take_down/take_down.md'
- 'Final word': 'pages/final_word.md'
- Cheat sheet:
- Bash: pages/cheat_sheet/bash/bash.md
- Git: pages/cheat_sheet/git/git.md
- Git official: pages/cheat_sheet/git/git_official.md
- Conda: pages/cheat_sheet/conda/conda.md
- Notebook: pages/cheat_sheet/notebook/notebook.md
- Docker: https://dockerlabs.collabnix.com/docker/cheatsheet/
- Ask a question: pages/slido.md