https://github.com/cnr-ibba/nf-neestimator
A nextflow pipeline for Current Effective Population Size (Ne) calculations with bootstrapping
Science Score: 13.0%
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Low similarity (5.4%) to scientific vocabulary
Keywords
Repository
A nextflow pipeline for Current Effective Population Size (Ne) calculations with bootstrapping
Basic Info
Statistics
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 1
- Releases: 1
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Metadata Files
README.md
nf-neestimator
A nextflow pipeline for Ne estimates with bootstrapping
Background
This pipeline is an attempt to call NeEstimator2 by bootstrapping individuals from a plink binary file. You require both nextflow and singularity (or docker) configured in order to call this pipeline properly
Calling pipeline
Simply type:
bash
nextflow run cnr-ibba/nf-neestimator -resume -profile singularity --prefix <plink file prefix>
where the --prefix parameter is the same prefix you would pass as plink --bfile
Customize configuration
This pipeline is configured for bootstrapping 10, 20 and 100 individuals 1000 times. If you need to customize the bootstrapping, you can create a custom configuration file like this:
conf
params {
prefix = '<plink file prefix>'
steps = 50
individuals = [10, 20, 30]
}
Add then provide this custom configuration file with the nextflow -config
parameter. See configuration file
in the nexflow documentation for more information
Owner
- Name: CNR-IBBA
- Login: cnr-ibba
- Kind: organization
- Location: Milan
- Website: https://www.ibba.cnr.it/
- Repositories: 25
- Profile: https://github.com/cnr-ibba
Bioinformatic Group @ CNR-IBBA
GitHub Events
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- Release event: 1
- Push event: 1
- Create event: 1
Last Year
- Release event: 1
- Push event: 1
- Create event: 1
Dependencies
- debian 11-slim build