nf-core pipeline · archived ·
nf-core/crisprvar
A Nextflow pipeline running CRISPResso to evaluate outcomes from genome editing experiments.
What nf-core/crisprvar is
nf-core/crisprvar is a bioinformatics workflow designed to evaluate the outcomes of genome editing experiments. It automates the execution of CRISPResso to analyse edits and sequence variations across experimental datasets.
The workflow was developed within the nf-core community using Nextflow and supports Docker and Singularity containerisation. The project was left as a work in progress and is now archived and no longer maintained.
What the pipeline does
The pipeline uses the Nextflow workflow management system to execute CRISPResso on genome editing experiment data. Analyses run inside Docker or Singularity containers to package dependencies and support portable execution across various computing environments.
Key facts
- Workflow tool
- Nextflow
- Core software
- CRISPResso
- Containers
- Docker, Singularity
- Status
- Archived — no longer maintained
What you can use it for
- Evaluating genome editing outcomes
- Running CRISPResso to inspect and quantify the genetic edits generated during genome editing experiments.
- Containerised editing analysis
- Executing CRISPResso workflows in reproducible environments using Docker or Singularity containers.
Strengths and limits
Good at
- Uses Docker and Singularity containers to deliver reproducible analysis environments.
- Built with Nextflow to provide portability across diverse computing infrastructures.
Watch out for
- The repository is archived and no longer maintained.
- The pipeline remained a work in progress prior to archival.
Questions
Can I run nf-core/crisprvar without my own cluster?
The research agent runs nf-core/crisprvar with Nextflow on its own machine — up to 32 cores, 256 GiB of memory and 24 hours per run, which covers the test profile and real single-sample runs. It builds the samplesheet, checks it against the pipeline's schema and reads the results back. When a run is too big for one machine, it gives you the exact command for your own cluster instead.
What licence is nf-core/crisprvar under?
MIT, like every nf-core pipeline.
Which tool does the pipeline use to analyse editing results?
The pipeline runs CRISPResso to evaluate experimental genome editing outcomes.
Is nf-core/crisprvar currently maintained?
No, the pipeline is archived and no longer under active maintenance.
What container environments does the pipeline support?
It provides support for Docker and Singularity containers.
Written from nf-core/crisprvar's own README. Statements citing a figure that does not appear there are removed before publication. Licence and running details come from our registry.