Multi image scenario

YAMP takes advantage of a multi-image scenario, which means that each analysis step uses a different container.

The list of used container is specified in the nextflow.config file, as follows:

• Docker:

  • FastQC: quay.io/biocontainers/bbmap:38.87--h1296035_0
  • BBmap: quay.io/biocontainers/fastqc:0.11.9--0
  • Biobakery: biobakery/workflows:3.0.0.a.6.metaphlanv3.0.7
  • QIIME2: qiime2/core:2020.8
  • MultiQC: quay.io/biocontainers/multiqc:1.9--py_1

• Singularity:

  • FastQC: https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0
  • BBmap: https://depot.galaxyproject.org/singularity/bbmap:38.87--h1296035_0
  • Biobakery: biobakery/workflows:3.0.0.a.6.metaphlanv3.0.7
  • QIIME2: qiime2/core:2020.8
  • MultiQC: https://depot.galaxyproject.org/singularity/multiqc:1.9--py_1

How do I pull these containers?

Technically, you don't have to do anything. Nexflow will pull all of them the first time you run YAMP.

However, the time required for their download will depend upon the speed of your internet connection and may hit the YAMP process wall time, especially if you are running one of the test profiles. In this case, you can pull the containers specified in the nextflow.config file in a folder of your choice beforehand, using one of the following commands (according to whether you are using Docker or Singularity):

docker pull image

or

singularity pull image

Please note that, if you are using Singularity, you will also have to tell Nextflow to look in the correct folder, as explained here.

What if I want to use different containers?

If you want to use your own containers, you can change the container specification in the nextflow.config file, or any Nextflow config file (more on this here).

You can familiarise yourself with the Nextflow configuration file and its scopes on the Nextflow documentation. Please also refer to the Nextflow documentation for more details about Docker and Singularity.

Please note that if you change software versions, some of the provided files (see Getting started) may no longer work.