nf-processes

scRNA-utils

modules and utility scripts for processing scRNA data

Installation

Installation requires the use of Nextflow, a workflow description language (WDL) that enables reproducible parallelization of common bioinformatics tasks. Nextflow provides an executable that requires both Groovy and Java/JDK. Installation of the portable executable is as follows:

wget -qO- https://get.nextflow.io | bash

or

curl -s https://get.nextflow.io | bash

More specific installation instructions for Nextflow can be found here.

Pipeline installation & Updating

git clone https://github.com/GaitiLab/scRNA-utils.git
git checkout main
git pull

Modules

Modules represent individual processes for dedicated single cell tasks, such as executing cellranger to running scrublet doublet detection on a series of matrices. They are designed to be run individually, or as part of a larger workflow/pipeline.

Modules can be run using the following generic command:

nextflow run scRNA-utils/modules/{module_selection}/ where the module_selection is the name of the specific module to be run. Currently the available modules can be found in the modules directory:

Running individual scRNA processing pipelines from modules

Within the modules directory are two basic pipelines for processing scRNA-seq data from raw FASTQ files:

Below are the links to the specific user documentation for each type of scRNA-seq data.

Running the split pipe pipeline for ParseBio data

parseBio split-pipe analysis pipeline
split-pipe instructions using Nextflow

Running the cellranger count pipeline for 10x Genomics scRNA data

cellranger count pipeline for 10X scRNA
cellranger instructions using Nextflow

Workflows

Workflows represent more complex and linked series of processes. Currently there is one workflow in development for toggling between both ParseBio and 10X scRNA data. The workflow can be found in workflows and enables the following behaviour:

Running combined/toggled scRNA processing pipelines from workflows

Currently under development.