Single‐cell RNA‐seq preprocessing nextflow pipeline (Iris)

Introduction

https://github.com/joechanlab/nf-scrnaseq

Steps

1. Load pre-installed nextflow conda environment

conda activate /usersoftware/chanj3/nextflow

2. Clone the Github repository

git clone https://github.com/joechanlab/nf-scrnaseq.git

3. Create the sample sheet and parameter YAML file

See https://github.com/joechanlab/nf-scrnaseq/blob/main/README.md

4. Run the pipeline

export NXF_SINGULARITY_CACHEDIR="/usersoftware/chanj3/singularity" # pre-downloaded singularity images
cd nf-scrnaseq
nextflow run ./main.nf -resume -profile iris -params-file <path to params.yml> -w "/scratch/chanj3/<MSKusername>/work"