Update README.md

Updated to reflect a all input arguments needed for each part of the pipeline.

Signed-off-by: Ian M. B. <99409346+iPsychonaut@users.noreply.github.com>

Author: iPsychonaut

README.md

@@ -1,3 +1,4 @@
+
 # FunDiS Pipeline
 
 FunDiS Pipeline is a suite of scripts intended to streamline the processing of Next-Generation Sequencing (NGS) data. The scripts can be run individually or as a whole to form a complete pipeline.
@@ -11,6 +12,11 @@ This application is designed to be run on a Linux/WSL environment and requires t
 - pandas
 - pysam
 - biopython
+- multiprocessing
+- math
+- queue
+- glob
+- shutil
 
 The application also relies on the following tools:
 
@@ -34,7 +40,7 @@ Each module of the pipeline can be run individually or as a whole.
 To run the whole pipeline, use the `fundis_main.py` script. For example:
 
 ```
-python /path/to/fundis_main.py -i /path/to/input.fastq -t /path/to/primers.txt -p 80
+python /path/to/fundis_main.py -i /path/to/input.fastq -x /path/to/index.txt -t /path/to/primers.txt -p 80
 ```
 
 ### Running Individual Modules
@@ -44,28 +50,28 @@ Each module can also be run individually. Here's what each module does:
 - **fundis_minibar_ngsid.py**: This script processes the input FASTQ file with MiniBar and NGSpeciesID. MiniBar is a tool for demultiplexing barcoded read data and NGSpeciesID is a tool used for the identification of specimens in NGS datasets. The script starts by checking the operating system, installing missing libraries, and setting up the working environment. It then moves on to demultiplexing and identifying species from the input FASTQ data. The results are output in a directory specified by the user.
 
 ```
-python /path/to/fundis_minibar_ngsid.py -i /path/to/input.fastq -t /path/to/primers.txt -p 80
+python /path/to/fundis_minibar_ngsid.py -i /path/to/input.fastq -x /path/to/index.txt -t /path/to/primers.txt -p 80
 ```
 
 - **fundis_haplotype_phaser.py**: This script takes the output from the `fundis_minibar_ngsid.py` script and phases the haplotypes for each sample. Phasing is the process of determining the specific set of variants found on each physical copy of a particular gene or genomic region. The phased haplotypes are output in the NGSpeciesID output directory.
 
 ```
-python /path/to/fundis_haplotype_phaser.py -i /path/to/input_directory -p 80
+python /path/to/fundis_haplotype_phaser.py -i /path/to/input_dir -p 80
 ```
 
-- **fundis_summarize2.py**: This script summarizes the output from the `fundis_haplotype_phaser.py` script. It provides a summary of the results, including counts of unique samples, total consensus sequences, and total reads in consensus sequences. It also copies and updates the names of all FASTQ and consensus FASTA files. The results are output in a summary directory named after the source directory.
+- **fundis_summarize.py**: This script summarizes the output from the `fundis_haplotype_phaser.py` script. It provides a summary of the results, including counts of unique samples, total consensus sequences, and total reads in consensus sequences. It also copies and updates the names of all FASTQ and consensus FASTA files. The results are output in a summary directory named after the source directory.
 
 ```
-python /path/to/fundis_summarize2.py -s /path/to/source_folder -p 80
+python /path/to/fundis_summarize.py -i /path/to/input_dir -p 80
 ```
 
 ## Arguments
 
-- `-i`, `--input_fastq`: Path to the FASTQ file containing ONT nrITS data.
+- `-i`, `--input_fastq` or `--input_dir`: Path to the FASTQ file containing ONT nrITS data or path to the directory containing the data.
 - `-t`, `--primers_text_path`: Path to Text file containing the Primers used to generate input_fastq.
-- `-p`, `--percent_system_use`: Percent system use written as integer.
-- `-s`, `--source_folder`: Path to the source folder.
+- '-x', '--minbar_index_path', type=str, help='Path to Text file containing the minibar index to parse input_fastq.
+- `-p`, `--percent_system_use`: Percent system use written as an integer.
 
 ## Author
 
-Ian Michael Bollinger (ian.michael.bollinger@gmail.com)
+Ian Michael Bollinger (ian.michael.bollinger@gmail.com/researchconsultants@critical.consulting)