CCBR / CRISPIN

CRISPR screen pipeline

CRISPIN 🍪

Crispr screen sequencing analysis pipeline

🚧 This project is under active development. It is not yet ready for production use. 🚧

Set up

CRISPIN is installed on the Biowulf HPC. For installation in other execution environments, refer to the docs.

Biowulf

CRISPIN is available on Biowulf in the ccbrpipeliner module. You'll first need to start an interactive session and create a directory from where you'll run crispin.

# start an interactive node
sinteractive --mem=2g --cpus-per-task=2 --gres=lscratch:200
# make a working directory for your project and go to it
mkdir -p /data/$USER/crisprseq
cd /data/$USER/crisprseq
# load the ccbrpipeliener module
module load ccbrpipeliner

Usage

Initialize and run crispin with test data:

# copy the crispin config files to your current directory
crispin init
# preview the crispin jobs that will run with the test dataset
crispin run --mode local -profile test -preview
# launch a crispin run on slurm with the test dataset
crispin run --mode slurm -profile test,biowulf

To run CRISPIN on your own data, you'll need to create a sample sheet. Take a look at the example: assets/samplesheet_test_biowulf.csv.

You'll also need to select an appropriate library for your dataset. CRISPIN is bundled with several libraries in assets/lib, or you can download your own. Once you've created a samplesheet with paths to your fastq files, run crispin with the --input option to specify the path to your sample sheet and --library for the path to your library file:

crispin run --mode slurm -profile biowulf --input samplesheet.csv --library assets/lib/yusa_library.csv

Help & Contributing

Come across a bug? Open an issue and include a minimal reproducible example.

Have a question? Ask it in discussions.

Want to contribute to this project? Check out the contributing guidelines.

References

This repo was originally generated from the CCBR Nextflow Template. The template takes inspiration from nektool¹ and the nf-core template. If you plan to contribute your pipeline to nf-core, don't use this template -- instead follow nf-core's instructions².

Footnotes

1. nektool https://github.com/beardymcjohnface/nektool ↩

2. instructions for nf-core pipelines https://nf-co.re/docs/contributing/tutorials/creating_with_nf_core ↩