Making the use of nextflow nfcore pipeline to process data

adapt in wwang's project setting

Features

• Run nf-core pipeline in singularity conda environment
• Limit the CPUs and memory usage
• Increase time limit for time-consuming steps

Installation

Install all requirments in conda

## set conda channels
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge

nextflow

## create an environment called nextflow and install nextflow
conda create --name nextflow nextflow
## actiavte the nextflow envrionment
conda activate nextflow

singularity

## install singularity in the same environment with nextflow
conda install -c conda-forge singularity

Reference

Tools	Link
nextflow	https://www.nextflow.io
nf-core	https://nf-co.re
singularity	https://anaconda.org/conda-forge/singularity