Docker benchmarks

This repository contains the benchmarks for these pipelines:

• Rnaseq-toy
• Nmdp-flow
• Piper-nf

Quick start

To reproduce the figures from raw data clone this repository:

git clone https://github.com/cbcrg/docker-benchmarks.git && cd docker-benchmarks

Then pull the required Docker image:

docker pull cbcrg/make-peerj5515

Finally launch the make script using the following command:

docker run -v $PWD:$PWD -w $PWD cbcrg/make-peerj5515 bash make-all.sh

(if you don't want or cannot use Docker, you will need to download and install the required dependencies: R, Datamash, Make and Groovy. See the included Dockefile for configuration details).

Structure of the repository

Benchmarks scripts and data are organised in separate folders depending the pipeline executed:

• Rnaseq-toy
• nmdp-flow
• piper-nf

Each of these folders contains a Makefile and other scripts used by it to generate the figures. Raw data of each executions are the files docker_{1..10}/trace.csv and native_{1..10}/trace.csv in the same folder.

The main files produced by the make process are:

• table.txt: the numbers included in the Table 1
• fig_correlation.png: the figure in included in the manuscript.

See the respective Makefiles for more details.

Replicate benchmarks

Pipeline executions can be replicated following the instructions in the respective repositories, listed below:

• nmdp-flow
• piper-nf
• rnaseq-toy