czbiohub-sf / CRISPRflow

MAGeCK analysis automated by Nextflow

CRISPRflow

MAGeCK analysis automated by Nextflow

modified based on https://github.com/FredHutch/crispr-screen-nf

System requirements

Linux, MacOS, Windows(WSL)

Dependencies

• Docker
• Java 11 (or later, up to 17)
• conda
• git

Usage:

One-time preparation work

clone the repository

git clone https://github.com/czbiohub/CRISPRflow.git

Go the repository directory, switch the branch if running branch other than master

cd CRISPRflow

Create conda environment and activate it

conda env create -f environment.yml
conda activate CRISPRflow

Pull docker images

bash helper_scripts/pull_docker_imgs.sh 

Make the nextflow command executable

chmod a+x ./nextflow

Process your fastq.gz files

Start the Docker program.

Check fastq files and create nextflow commands

conda activate CRISPRflow
python helper_scripts/check_files_and_get_nf_cmds.py --xlsx metadata/Naming_convention_example.xlsx

You should see the following output:

Start nextflow

bash Naming_convention_example.xlsx.sh

You should see the following output:

Input

• Fastq files
• A reference library file for each (sub)library
• A xlsx file that contains metadata and design of the analysis (example file: metadata/Naming_convention_example.xlsx)
  The metadata xlsx file will automatically generate path + names for the fastq.gz files, please make sure to move and rename your fastq.gz files accordingly

Library reference files

For file format, see MAGeCK manual: https://sourceforge.net/p/mageck/wiki/Home/

Troubleshooting

• Java issues (after installing java):
  For most case, it can be fixed by explicitly specifying the version installed (v17 in the example)

unset JAVA_HOME
export JAVA_HOME=`/usr/libexec/java_home -v 17`

• Error "executing process ... The command 'docker' could not be found ..."
  You'll need to start the docker program on your computer

• Error "Both treatment and control are in the file name", but it's not the case
  Captalize the first letter of your treatment names, for example: Infected, Uninfected