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mkdocs.yml
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mkdocs.yml
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# \DOCS\-------------------------------------------------------------------------
#
# CONTENTS : MkDocs
#
# DESCRIPTION : none
#
# RESTRICTIONS : none
#
# REQUIRES : none
#
# ---------------------------------------------------------------------------------
# Copyright (c) 2018-2021, Pay Giesselmann, Max Planck Institute for Molecular Genetics
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in all
# copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
# SOFTWARE.
#
# Written by Pay Giesselmann
# ---------------------------------------------------------------------------------
site_name: Nanopype Documentation
site_description: 'Snakemake pipelines for nanopore sequencing data archiving, processing and analysis'
site_author: 'Pay Giesselmann'
site_url: 'https://nanopype.readthedocs.io'
copyright: 'Copyright © 2018 - 2019 Pay Giesselmann, Max Planck Institute for Molecular Genetics'
repo_name: 'giesselmann/nanopype'
repo_url: 'https://github.com/giesselmann/nanopype/'
docs_dir: docs
# plugins:
# - search
# - pdf-export:
# verbose: true
# combined: false
# media_type: print
# enabled_if_env: ENABLE_PDF_EXPORT
theme:
name: 'material'
include_search_page: false
search_index_only: true
icon:
logo: material/apps
static_templates:
- 404.html
# Extensions
markdown_extensions:
- markdown.extensions.admonition
- markdown.extensions.codehilite:
guess_lang: false
- markdown.extensions.def_list
- markdown.extensions.footnotes
- markdown.extensions.meta
- markdown.extensions.toc:
permalink: true
- pymdownx.arithmatex
- pymdownx.betterem:
smart_enable: all
- pymdownx.caret
- pymdownx.critic
- pymdownx.details
- pymdownx.inlinehilite
- pymdownx.keys
- pymdownx.magiclink
- pymdownx.mark
- pymdownx.smartsymbols
- pymdownx.superfences
- pymdownx.tasklist:
custom_checkbox: true
- pymdownx.tilde
# Page tree
nav:
- Introduction: index.md
- Tools in Nanopype: tools.md
- Installation:
- Prerequisites: installation/prerequisites.md
- Singularity: installation/singularity.md
- Source: installation/src.md
- Docker: installation/docker.md
- Configuration: installation/configuration.md
- Tests: installation/test.md
- Update: update.md
- Workflow:
- General: usage/general.md
- Cluster computing: usage/cluster.md
- Modules:
- Storage: rules/storage.md
- Basecalling: rules/basecalling.md
- Alignment: rules/alignment.md
- Assembly: rules/assembly.md
- Methylation: rules/methylation.md
- Transcriptome: rules/transcript.md
- Structural Variation: rules/sv.md
- Demultiplexing: rules/demux.md
- Report: rules/report.md
- Plugins:
Intro: plugins/intro.md
Winnowmap: plugins/winnowmap.md
- Tutorial:
- Intro : examples/intro.md
- Data Import: examples/import.md
- Alignment : examples/align.md
- Structural Variation: examples/sv.md
- Isoform Detection: examples/iso.md
# - Nanopolish: examples/nanopolish.md
# - Barcoding: examples/demux.md
- Contribution: contribute.md
- Release Notes: release-notes.md
- Citation: citation.md
- License: license.md