Stable 1.0.0

README.md

@@ -18,7 +18,9 @@ A complete documentation is available [MMAseq Documentation](https://ssi-dk.gith
 Please to report bugs or enhancement use the Issue Tracker. 
 
 # Citation
-When using SSI analysis in published work, please cite the following...
+When using SSI analysis in published work, please cite the following:
 
+[PLACEHOLDER FOR CITATION INSTRUCTION]
 
-For citations of included algorithms and sub-modules please see the (placeholerreferences).
+
+For citations of included algorithms and sub-modules please see the [references](https://ssi-dk.github.io/MMASeq/references/)

docs/description.md

@@ -9,17 +9,29 @@ The input data is specified through a samplesheet, which allows for batch proces
 
 ## Repository Structure
 
-Within the `mmaseq` folder repository, the project is organized into several key directories and files that facilitate the workflow and its management:
+Within the `MMAseq` folder repository, the project is organized into several key directories and files that facilitate the workflow and its management:
 
-### `workflow/`
+### `src/`
 
-:   Contains all Snakemake-related files: rule definitions, species-specific configs, conda environments, and helper scripts.
+:   It is the top level directory that contains all snakemake-related files: rule definitions, species-specific configs, conda environments, and helper scripts.
 
-### `data/`
-:   Includes test data and template samplesheets to demonstrate pipeline functionality and structure.
+### `docs/`
+:   Includes the the markdow documentation files and assets, used to build the project documentation.
 
-### `config/`
-:   Stores the main configuration file, metadata and the results catalogue.
+### `LICENSE` 
+:   The `LICENSE` file contains the terms under which the software is distributed, specifying the permissions and limitations for users of the software.
+
+### `README.md`
+:   The`README.md` provides an overview of the project and other relevant information for users.
+
+### `mkdocs.yml`
+:   The `mkdocs.yml` file is the configuration file for MkDocs, a static site generator used to build the project documentation. It defines the structure and settings for the documentation site.
+
+### `pyproject.toml`
+:   The `pyproject.toml` file is a configuration file for Python projects, specifying the project metadata, dependencies, and build system requirements. It is used to manage the Python environment and dependencies for the project, ensuring that all necessary packages are installed and compatible with the workflow.
+
+### `version_guide.md`
+:   The `version_guide.md` file provides information about the versioning strategy and release notes for the project.
 
 <details>
 <summary><strong>Click to expand: Full project tree structure </strong></summary>
@@ -30,26 +42,36 @@ Within the `mmaseq` folder repository, the project is organized into several key
 ├── README.md
 ├── mkdocs.yml
 ├── pyproject.toml
-├── mmaseq/
-    ├── config/
-        |   ├── target_screening/              # Metadata Folder
-        |   ├── species_configs/               # Folder containing all species configuration file
-        |   ├── results_catalogue.yaml         # File containing all the information regarding the                  
-        |   ├── config.yaml                    # Main pipeline default configuration file                 
-        ├── data/
-        │   ├── assemblies/                    # Example assemblies  
-        |   ├── reads/                         # Reads folder
-        |   |    └── dl_script.sh              # Script to download test reads
-        │   └── samplesheet.tsv                # Example input sheet
-        │                          
-        ├── workflow/
-        │   ├── Snakefile                      # Main Snakemake workflow definition
-        │   ├── envs/                          # Folder containing all environments configuration files 
-        │   ├── rules/                         # Folder containing all snakemake rules 
-        │   └── scripts/                       # Folder containing all helper scripts
-        ├── helper_functions.py                # Helper functions used in the launcher
-        └── mmaseq.py                          # Main launcher of the pipeline
-
+├── version_guide.md
+├── src
+    ├── mmaseq/
+        ├── config/
+            |   ├── target_screening/              # Metadata Folder
+            |   ├── species_configs/               # Folder containing all species configuration file
+            |   ├── results_catalogue.yaml         # File containing all the information regarding the results generated by the pipeline                 
+            |   ├── Test.yaml                    # Main pipeline default configuration file                 
+            ├── data/
+            │   ├── assemblies/                    # Example assemblies  
+            |   ├── reads/                         # Reads folder
+            |   |    └── reads.urls                # Example input reads urls file
+            │   ├── samplesheet_small.tsv          # Reduced example input sheet
+            │   └── samplesheet.tsv                # Complete example input sheet
+            │                          
+            ├── workflow/
+            │   ├── Snakefile                      # Main Snakemake workflow definition
+            │   ├── envs/                          # Folder containing all environments configuration files 
+            │   ├── rules/                         # Folder containing all snakemake rules 
+            │   └── scripts/                       # Folder containing all helper scripts
+            ├── utils/                             # Folder containing all helper functions and classes
+            |   ├── PATH.py                        # File containing all paths used in the pipeline
+            |   ├── helpers.py                     # File containing helper functions and classes    
+            |   ├── logging_setup.py               # File containing the logging setup for the pipeline  
+            |   ├── results_paths.py               # File containing the functions to generate the paths for the results generated by the pipeline
+            |   ├── results_aggregator.py          # File containing the functions to aggregate the results generated by the pipeline
+            |   └── sample_config.py               # File containing the functions to parse the sample configuration files 
+            ├── deploy.py                          # Script to deploy the pipeline into a specified location and run the pipeline on a test dataset
+            └── mmaseq.py                          # Main launcher of the pipeline
+
 ``` 
 
 </details>