update docs

docs/workflows/standalone/dorado_basecalling.md

@@ -8,39 +8,39 @@
 
 ## Dorado Basecalling Overview
 
-The Dorado Basecalling workflow is used to convert Oxford Nanopore `POD5` sequencing files into `FASTQ` format by utilizing a GPU-accelerated environment. This workflow is ideal for high-throughput applications where fast and accurate basecalling is essential.
+The Dorado Basecalling workflow is used to convert Oxford Nanopore `POD5` sequencing files into `FASTQ` format by utilizing a GPU-accelerated environment. This workflow is ideal for high-throughput applications where fast and accurate basecalling is essential. The workflow will upload fastq files to a user designated terra table for downstream analysis.
 
 ### Model Type Selection
 
 Users can choose between automatic or manual model selection using a configurable use_auto_model flag:
 
-- Automatic Model Selection: Automatically picks the best model ('sup', 'hac', or 'fast') based on the input file and user-defined model accuracy paramater.
+Automatic Model Selection: Automatically picks the best model ('sup', 'hac', or 'fast') based on the input file and user-defined model accuracy paramater.
 
-- Manual Model Input: If the user disables automatic selection, a specific model path or model version must be provided.
+Manual Model Input: If the user disables automatic selection, a specific model path or model version must be provided.
 
 - **Model Type (sup):** (super accuracy) The most accurate model, recommended for critical applications requiring the highest basecall accuracy. It is the slowest of the three model types.
 - **Model Type (hac):** (High Accuracy) A balance between speed and accuracy, recommended for most users. Provides accurate results faster than `sup` but less accurate than `sup`.
 - **Model Type (fast):** (Fast Model) The fastest model, recommended when speed is prioritized over accuracy, such as for initial analyses or non-critical applications.
 
-**Example Manual Models:**
+### Example Manual Models:
 - `[email protected]`
 - `[email protected]`
 - `[email protected]`
 
-## **Workflow Structure**
+### Workflow Structure
 
-1. **Dorado Basecalling**: Converts `POD5` files to **SAM** files using the specified model.
+1. **Dorado Basecalling**: Converts `POD5` files to 'SAM' files using the specified model.
 2. **Samtools Convert**: Converts the generated SAM files to BAM for efficient processing.
 3. **Dorado Demultiplexing**: Demultiplexes BAM files to produce barcode-specific FASTQ files.
 4. **FASTQ File Transfer**: Transfers files to Terra for downstream analysis.
 5. **Terra Table Creation**: Generates a Terra table with the uploaded FASTQ files for downstream analyses.
 
 ---
 
-## **Inputs**
+## Inputs
 
 | **Task** | **Variable** | **Type** | **Description** | **Default Value** | **Required** |
-|---|---|---|---|---|---|---|
+|---|---|---|---|---|---|
 | Basecalling | **input_files** | Array[File] | Array of `POD5` files for basecalling | None | Yes |
 | Basecalling | **use_auto_model** | Boolean | Use automatic model selection (`sup`, `hac`, or `fast` based on model accuracy)| true | No |
 | Basecalling | **model_accuracy** | String | Desired model accuracy (`sup`, `hac`, `fast`) if using automatic selection | sup | No |
@@ -58,18 +58,21 @@ Users can choose between automatic or manual model selection using a configurabl
 
 ---
 
-### **Detailed Input Information**
+### Detailed Input Information
 - **fastq_file_name**: This will serve as a prefix for the output FASTQ files. For example, if you provide `project001`, the resulting files will be named `project001_barcodeXX.fastq.gz`.
 - **kit_name**: Ensure the correct kit name is provided, as it determines the barcoding and adapter trimming behavior.
 - **fastq_upload_path**: This is the folder path in Terra where the final FASTQ files will be transferred for further analysis. Ensure the path matches your Terra workspace configuration.
 
 ---
 
-## **Outputs**
+## Outputs
 
 | **Variable** | **Type** | **Description** |
-|---|---|---|---|
+|---|---|---|
 | **basecalled_fastqs** | Array[File] | Array of FASTQ files generated from basecalling |
 | **demuxed_fastqs** | Array[File] | FASTQ files produced from BAM demultiplexing |
 | **logs** | Array[File] | Log files from the demultiplexing process |
 | **terra_table_tsv** | File | TSV file for Terra table upload |
+
+<!-- -->
+><https://github.com/nanoporetech/dorado/>