A simple Nextflow pipeline for testing the performance of sambamba vs samtools.
Note: the pipeline can be used without a container engine by installing the required versions of sambamba and samtools in your system.
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