Overview¶

The scRNA github repository is stored locally, and will be used for project deployment. Multiple projects can be deployed from this one point simultaneously, without concern.

1. Getting Started¶

1.1 Introduction¶

The scRNA Pipeline begins at various stages, depending on the users needs. The pipeline can begin with GEX FASTQ files, performing cell counting, with 10X Genomics CellRanger. Then, normalization and pre-processing occurs, using custom R scripts with packages like Seurat. Alternatively the user can begin with .h5 files, beginning the pipeline post-preprocessing.

1.2 Setup Dependencies¶

scRNA has several dependencies listed below. These dependencies can be installed by a sysadmin. All dependencies will be automatically loaded if running from Biowulf.

nextflow: "nextflow/23.04.1"
cellranger "cellranger:7.1.0"
R: "R/4.3"

Docker containers to run the pipeline are currently in development.

scRNA has been exclusively tested on Biowulf HPC. Log in to the cluster's head node and move into the pipeline location.

# ssh into cluster's head node
ssh -Y $USER@biowulf.nih.gov

1.4 Load an interactive session¶

An interactive session should be started before performing any of the pipeline sub-commands, even if the pipeline is to be executed on the cluster.

# Grab an interactive node
sinteractive --mem=64g --cpus-per-task=16 --time=8:00:00 --gres=lscratch:128

1.5 Installing and setting up SINCLAIR¶

The ccbrpipeliner module on Biowulf also loads module dependencies, and should be loaded prior to running SINCLAIR:

module load ccbrpipeliner/8

Initialize the output directory for SINCLAIR. This will create a new directory and copy the necessary files to run the pipeline:

sinclair init --output /path/to/output/dir

From here, proceed to preparing the files and then running the pipeline.