Add notebook to sphinx

docs/requirements.txt

@@ -1,3 +1,4 @@
 sphinx
+nbsphinx
 myst-parser
 furo

docs/source/conf.py

@@ -3,7 +3,8 @@
 author = 'Fabiola Curion, Xichen Wu, Lukas Heumos'
 release = '1.0.0'
 
-extensions = ['myst_parser']
+extensions = ['myst_parser',
+              'nbsphinx']
 
 source_suffix = {
     '.rst': 'restructuredtext',
@@ -13,8 +14,9 @@
 
 templates_path = ['_templates']
 
-exclude_patterns = []
+exclude_patterns = ['_build', '**.ipynb_checkpoints']
 
 html_theme = "furo"
+html_static_path = ['_static']
 
-html_static_path = ['_static']
+nbsphinx_execute = 'never'

notebook.ipynb → docs/source/hadge_output.ipynb

@@ -1,5 +1,12 @@
 {
  "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Working with hadge output"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 1,
@@ -16,7 +23,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "This notebook serves to get familiar with the ouput of hadge and reproduce some figures from the manuscript."
+    "This notebook serves to get familiar with the output of hadge and reproduce some figures from the manuscript."
    ]
   },
   {

docs/source/index.md

@@ -56,7 +56,7 @@ nextflow run main.nf -profile test
 
 ## Notebook
 
-Check[](../../notebook.ipynb) to get familiar with the output of hadge.
+Check[](hadge_output.ipynb) to get familiar with the output of hadge.
 
 ## **Pipeline output**
 
@@ -98,6 +98,7 @@ general
 genetic
 hashing
 rescue
+hadge_output
 ```
 
 # Indices and tables