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crispin

CRISPR screen pipeline

https://github.com/ccbr/crispin

Science Score: 67.0%

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    CITATION.cff file
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    .zenodo.json file
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    DOI references
    Found 3 DOI reference(s) in README
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    Academic publication links
    Links to: zenodo.org
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    Low similarity (15.8%) to scientific vocabulary
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Repository

CRISPR screen pipeline

Basic Info
Statistics
  • Stars: 0
  • Watchers: 3
  • Forks: 3
  • Open Issues: 14
  • Releases: 7
Created almost 3 years ago · Last pushed about 1 year ago
Metadata Files
Readme Changelog Contributing License Citation

README.md

CRISPIN 🍪

CRISPr screen sequencing analysis pipelINe

formerly known as CRUISE

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

build docs DOI release

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.

```sh

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:

```sh

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/samplesheettestbiowulf.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:

sh 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 nektool[^1] 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 instructions[^2].

[^1]: nektool https://github.com/beardymcjohnface/nektool [^2]: instructions for nf-core pipelines https://nf-co.re/docs/contributing/tutorials/creatingwithnf_core

Owner

  • Name: CCR Collaborative Bioinformatics Resource
  • Login: CCBR
  • Kind: organization
  • Email: nciccbr@mail.nih.gov
  • Location: United States of America

CCR Collaborative Bioinformatics Resource, Center for Cancer Research (NCI), National Institutes of Health

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "Please cite CRISPIN as below:"
authors:
  - family-names: Wong
    given-names: Nathan
    orcid: https://orcid.org/0000-0002-8882-3401
  - family-names: Sovacool
    given-names: Kelly
    orcid: https://orcid.org/0000-0003-3283-829X
  - family-names: Sevilla
    given-names: Samantha
    orcid: https://orcid.org/0000-0002-8734-9875
  - family-names: Koparde
    given-names: Vishal
    orcid: https://orcid.org/0000-0001-8978-8495
title: "CRISPIN: CRISPR screen pipeline"
url: https://ccbr.github.io/CRISPIN
repository-code: https://github.com/CCBR/CRISPIN
license: MIT
type: software
identifiers:
  - description: Archived snapshots of all versions
    type: doi
    value: 10.5281/zenodo.13844209
version: v1.2.1
date-released: "2025-05-28"

GitHub Events

Total
  • Create event: 21
  • Issues event: 6
  • Release event: 4
  • Delete event: 19
  • Member event: 1
  • Issue comment event: 5
  • Push event: 42
  • Pull request event: 27
Last Year
  • Create event: 21
  • Issues event: 6
  • Release event: 4
  • Delete event: 19
  • Member event: 1
  • Issue comment event: 5
  • Push event: 42
  • Pull request event: 27

Dependencies

.github/workflows/build.yml actions
  • actions/checkout v3 composite
  • actions/setup-python v4 composite
  • nf-core/setup-nextflow v1 composite
.github/workflows/docker.yml actions
  • actions/checkout v4 composite
  • docker/build-push-action v4 composite
  • docker/login-action v2 composite
  • hellofresh/action-changed-files v3 composite
  • pietrobolcato/action-read-yaml 1.0.0 composite
.github/workflows/docs.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
.github/workflows/projects.yml actions
docker/bagel/meta.yml cpan
docker/drugz/meta.yml cpan
modules/CCBR/cutadapt/meta.yml cpan
docker/bagel/Dockerfile docker
  • nciccbr/ccbr_ubuntu_base_20.04 v5 build
docker/drugz/Dockerfile docker
  • nciccbr/ccbr_ubuntu_base_20.04 v5 build
docs/requirements.txt pypi
  • mkdocs-git-revision-date-localized-plugin ==1.2.0
  • mkdocs-git-revision-date-plugin ==0.3.2
  • mkdocs-material ==9.1.6
  • mkdocs-material-extensions ==1.1.1
  • mkdocs-minify-plugin ==0.6.4
pyproject.toml pypi
  • Click >= 8.1.3
  • pyyaml >= 6.0
setup.py pypi