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README.md

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 The `scrnabox.slurm` is a single-cell RNA sequencing (scRNAseq) pipeline specifically designed for analyzing data under a High-Performance Computing (HPC) systems  using the Slurm Workload Manager ([slurm work load manager system](https://slurm.schedmd.com/)). The pipeline has been extensively utilized on the Digital Research Alliance of Canada's  [Beluga](https://docs.alliancecan.ca/wiki/B%C3%A9luga) cluster. ScRNAbox provides two distinct, yet high comparable Analysis Tracks: 
 1. [Cell Hashtags]()
 2. [Standard scRNA-seq]()
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 The Standard Analysis Track is designed for experiments where each sample is captured and sequenced separately, while the Cell Hashtag Analysis Track is designed for multiplexed experiments, whereby samples are tagged with sample-specific barcodes, pooled, and sequenced together. The Cell Hashtag Analysis Track is distinguished by an additional sample demultiplexing Step that assigns cells to their sample-of-origin via the sample-specific barcodes.   
 
 you can find comprehensive instructions on how to utilize the pipeline for [Cell Hashtags]() and [Standard scRNA-seq](), the pipeline provides detailed guidance on processing and analyzing these specific types of single-cell RNA sequencing (scRNA-seq) data.