How to use Docker

This tutorial explains how to use YAMP with Docker.

YAMP and Docker

YAMP takes advantage of a multi-image scenario. This means that each process will specify which container should be used, along with its version (as explained in the Multi image scenario tutorial).

YAMP also provides a docker profile that can be used to tell Nextflow to enable the use of Docker, as in the following example:

nextflow run YAMP.nf --reads1 myfile_R1.fq.gz --reads2 myfile_R2.fq.gz --prefix my_sample  
   --outdir output_folder --mode complete -profile base,docker

The docker profile is defined (along with all the other Nextflow YAMP profiles) in the nexflow.config file as follow:

docker.enabled = true

More information on YAMP preset profiles and how to create and combine them are available here.

A word of caution

Nextflow should be installed independently as explained here.

Nextflow orchestrates, in a transparent fashion, the flow of the pipeline by wrapping and executing each step using the docker run command. Thus, Nextflow lies outside the container, which is responsible for instantiating.

You can find more information about Docker containers and Nextflow here.

Troubleshooting

If you get this error:

Command error:
WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.

please decomment the following line: docker.runOptions = "--memory-swap '-1'" in the nextflow.config file. Thanks to Flavia Flaviani for identifying and solving this problem.

Retro compatibility

YAMP multi-image scenario and docker profile were introduced in version 0.9.5. The yampdocker file provided with previous versions is no longer compatible but mostly outdated and should not be used. If this is a problem for you, please open an issue and we will try to help.