DOC: move conf.py and index.rst into doc subdir

docs/conf.py

+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+project = 'MAGATT'
+copyright = '2024, Helene Rimbert'
+author = 'Helene Rimbert'
+release = '1.3'
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = ["myst_parser"]
+
+templates_path = ['_templates']
+exclude_patterns = []
+
+source_suffix = {
+	'.rst': 'restructuredtext',
+	'.txt': 'markdown',
+	'.md': 'markdown',
+}
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = 'sphinx_rtd_theme'
+html_static_path = ['_static']
+

docs/index.rst

+.. MAGATT documentation master file, created by
+   sphinx-quickstart on Thu Jan  4 15:41:34 2024.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to MAGATT's documentation!
+==================================
+
+Marker Assisted Gene Annotation Transfert for Triticeae.  
+
+Snakemake pipeline used to transfert GFF annotation on a new assembly with a fine target mapping approach.  
+
+.. toctree::
+   :maxdepth: 2
+   :titlesonly:
+   :caption: Installation
+
+   docs/install
+
+
+.. toctree::
+   :maxdepth: 2
+   :titlesonly:
+   :caption: Configuration
+
+   docs/pipeline_conf