A utility script for filtering the bedGraph files

This little script parallelizes the bedtools intersect utility for filtering the bedGraph files.

Pre-requisites

• Nextflow
• Conda

Usage

nextflow pull https://github.com/wal-yan/bed_filter

Options

Input samplesheet

The structure of samplesheet is very minimal since it only requires source and target columns as shown below

sample,bedGraph
sample-1,/path/to/sample-1.bedGraph
sample-2,/path/to/sample-2.bedGraph

Then refer that while invoking the pipeline

nextflow run https://github.com/wal-yan/bed-filter --samplesheet /path/to/samplesheet.csv

Customizing the script

To customize these scripts, you can take a look at the available parameters in ./nextflow.config file and then override them using a local config file, in a directory where you'd like to launch the pipeline.

Citation

Please use the Github citation page to cite this wrapper in your research.

Contribution

If you have specific requirements, you are encouraged to fork/clone and update your version to accomodate your needs.

Contribution, in all forms, is most welcome!