README.md

FunVCF

Fun Tools for VCF

I have a blog written explain the thinking behind this. See How to make a python script scale on Cloud?

VCF Cutter

VCF cutter reads a VCF and writes a new VCF which only contains SNV.

Run with Python

1. Get Docker from Docker Hub

   docker pull oxfordmmm/funvcf:v0.1.0

2. Install nextflow if not exists

See Nextflow Documentation

3. Run tests

nextflow run vcf-python.nf --input data/ --pattern *.vcf --output tests-python -profile docker
nextflow run vcf-python.nf --input data/ --pattern *.vcf --output tests-python -with-singularity funvcf-v0.1.0.img

Run with C++

1. Install nextflow if not exists

See Nextflow Documentation

2. Run tests

nextflow run vcf-cpp.nf --input data/ --pattern *.vcf --output tests-cpp -profile standard

Run with Nim

1. Install nextflow if not exists

See Nextflow Documentation

2. Run tests

nextflow run vcf-nim.nf --input data/ --pattern *.vcf --output tests-nim -profile standard