sc-analysis-nf

Pipeline to preprocess raw data from iRODS, developed using Nextflow (DSL=2)

Installation

All setup required to utilise the pipeline.

1. Clone the repository into local files

    git clone [email protected]:haniffalab/sc-analysis-nf.git
    cd [path/of/project/repo]
   

2. Create conda environment with Nextflow

    conda create -n nextflow_env -f environment.yml
    conda acitvate nextlfow_env 
   

Execution

Execute the pipeline

    nextflow run main.nf -c nextflow.config