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 Pipelie beings at various stages, depending on the users needs. The pipeline can begin with GEX FASTQ files, performing cell counting, with 10X Genomic's 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. [TODO: add as we go!]

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. Login 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 --time=12:00:00 --mem=8gb  --cpus-per-task=4 --pty bash

Overview¶

1. Getting Started¶

1.1 Introduction¶

1.2 Setup Dependencies¶

1.3 Login to the cluster¶

1.4 Load an interactive session¶