guigolab / sambamBench-nf

A simple Nextflow pipeline for testing the performance of sambamba vs samtools

sambamBench-nf

A simple Nextflow pipeline for testing the performance of sambamba vs samtools.

Requirements

• Nextflow 0.27.x (or higher)
• Java 8 or higher
• Docker 1.10 (or higher) or Singularity engine

Note: the pipeline can be used without a container engine by installing the required versions of sambamba and samtools in your system.

Quickstart

Install Nextflow with the following command:

curl -fsSL get.nextflow.io | bash

Run the pipeline with:

nextflow run guigolab/sambamBench-nf

Note: the command above will automatically download a test BAM file of ~4GB in ./data if the file is not present.

Check the Makefile for more commands.

The Nextflow config file contains the pipeline configuration including parameters and resource specifications.

A sample report of a run in the CRG cluster on a single node with 16 cpus and 120G of memory can be seen here