Improve documentation and tutorial

README.md

@@ -148,9 +148,10 @@ In both formats, the `--contigs` argument should specify a FASTA file containing
 Binette results are stored in the `results` directory. You can specify a different directory using the `--outdir` option.
 
 In this directory you will find:
-- `final_bins_quality_reports.tsv`: This is a TSV (tab-separated values) file containing quality information about the final selected bins.
-- `final_bins/`: This directory stores all the selected bins in fasta format.
-- `temporary_files/`: This directory contains intermediate files. If you choose to use the `--resume` option, Binette will utilize files in this directory to prevent the recomputation of time-consuming steps.
+- **`final_bins_quality_reports.tsv`**: This is a TSV (tab-separated values) file containing quality information about the final selected bins.
+- **`final_bins/`**: This directory stores all the selected bins in fasta format.
+- **`input_bins_quality_reports/`**: A directory storing quality reports for the input bin sets, with files following the same structure as `final_bins_quality_reports.tsv`.
+- **`temporary_files/`**: This directory contains intermediate files. If you choose to use the `--resume` option, Binette will utilize files in this directory to prevent the recomputation of time-consuming steps.
 
 
 The `final_bins_quality_reports.tsv` file contains the following columns:

docs/tutorial/analyse_binette_result.ipynb

@@ -7,7 +7,9 @@
    "source": [
     "## Analyse Binette results\n",
     "\n",
-    "Let's visualize the results from Binette and compare them to the initial bin sets used as input. "
+    "Let's visualize the results from Binette and compare them to the initial bin sets used as input. \n",
+    "\n",
+    "To explore these results interactively, you can open the Jupyter notebook via Binder by following this link: [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/genotoul-bioinfo/Binette/binder_tutorial_env?urlpath=git-pull%3Frepo%3Dhttps%253A%252F%252Fgithub.com%252Fgenotoul-bioinfo%252FBinette%26urlpath%3Dtree%252FBinette%252Fdocs%252Ftutorial%252Fanalyse_binette_result.ipynb%26branch%3Dmain)"
    ]
   },
   {
@@ -31,7 +33,8 @@
     "from pathlib import Path\n",
     "import plotly.express as px\n",
     "\n",
-    "# This is needed to properly display Plotly graphs in the documentation\n",
+    "# The following two lines are needed to properly display Plotly graphs in the documentation\n",
+    "# However you may need to remove these lines and restart the kernel to visualise the graph in another context\n",
     "import plotly.io as pio\n",
     "pio.renderers.default = \"sphinx_gallery\""
    ]
@@ -949,7 +952,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.19"
+   "version": "3.8.12"
   }
  },
  "nbformat": 4,

docs/tutorial/get_dataset.md

@@ -24,7 +24,7 @@ Once the tool is installed, you can download the "Kickstart" dataset with the fo
 
    ```{code-block} bash
    # Select the header of the table
-   head -n7 coal-metagenomics.tsv > coal-metagenomics_Kickstart_only.tsv
+   head -n8 coal-metagenomics.tsv > coal-metagenomics_Kickstart_only.tsv
 
    # Append the relevant line for the Kickstart dataset
    grep SRR5058924 coal-metagenomics.tsv >> coal-metagenomics_Kickstart_only.tsv