mumflow

A nextflow pipeline to run the mummer pipelines (align genomes, call snps) and process outputs into sane formats.

Mumflow pairwise aligns a number of assembled genomes to a set of reference genomes, and outputs common results for presence absence variant (PAV), snp, and repeat finding in standard formats.

Requirements

The pipeline uses Nextflow to execute tasks. Main steps require samtools, mummer (version >= 4), and bedtools. Scripts require python (Version >=3.5) and R (version >=3.5). Required R packages are R ape, tidyr, and circlize.

A singularity container providing all dependencies is available at https://cloud.sylabs.io/library/darcyabjones/default/mumflow#. To install singularity see the latest docs or see if your package manager has it available. To build the container yourself you will need version >=3.2. Running the build container should work with any version >= 3.0.

To pull the container run...

#NB its usually a good idea to take note of the actual latest version number.
singularity pull library://darcyabjones/default/mumflow:latest

Usage

nextflow run mumflow -resume --references "refs/*.fasta" --genomes "genomes/*.fasta"

To use a pulled singularity container...

singularity pull library://darcyabjones/default/mumflow:v0.0.2
nextflow run mumflow -resume -with-singularity ./mumflow_v0.0.2.sif --references "refs/*.fasta" --genomes "genomes/*.fasta"