nf-CRISPResso

A Nextflow workflow for CRISPResso.

This repository contains resources for integrating CRISPResso2 into your Nextflow projects.

For more information on Nextflow, refer to the Nextflow documentation.

Workflow Structure

• /workflows/CRISPResso/main.nf contains processes for:
  • CRISPResso
  • CRISPRessoBatch
  • CRISPRessoPooled
  • CRISPRessoWGS
• main.nf provides an example workflow demonstrating how to use CRISPResso processes.

Usage

A main.nf file like this:

include { CRISPResso } from './workflows/CRISPResso'


params.input_dir = './data'

workflow {
    CRISPResso(Channel.fromPath(params.input_dir))
}

can be executed like this:

nextflow main.nf --r1 ./input_dir/FANC.Cas9.fastq --auto

• Nextflow will use your local installation of CRISPResso, for example in a Conda environment.
• CRISPResso processes expect a path to the directory containing all data files as an input channel which is named input_dir in the CRISPResso nextflow process.
• All CRISPResso parameters can be passed through the command line using --param value or set in nextflow.config.
• ALL parameters passed through the command line must use two dashes ('--'). Note: this differs from standard command line usage of CRISPResso, for example -r1 must be passed to Nextflow as --r1.