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Nextflow and Seqera Containers

Seqera Containers is a free, publicly available bioinformatics container solution launched by Seqera in collaboration with AWS that allows researchers to generate custom containers on demand for any combination of Conda and PyPI packages at the click of a button.

This guide describes how to provision containers that include Conda packages through Seqera Containers and use them directly in your Nextflow pipelines. It includes:

  • Requesting a Conda package from Seqera Containers.
  • Creating a Nextflow pipeline that uses the container.
  • Running the Nextflow pipeline.
Prerequisites

You will need the following to get started:

Request a Conda package from Seqera Containers​

Seqera Containers enables users to generate custom Docker or Singularity containers by selecting Conda and PyPI packages through a web interface.

To request a Conda package from Seqera Containers:

  1. Open Seqera Containers in a browser.
  2. In the search box, enter samtools.
  3. In the search results, select Add in the bioconda::samtools result, and then Get Container to initiate the container build.
  4. From the Fetching container modal, copy the container image URI that Seqera Containers provides.
  5. Optional: Select View build details to watch Seqera Containers build the requested container in real time.

Create a Nextflow pipeline that uses the container​

Nextflow can use the container that Seqera Containers built in the previous section. Use the container URI from Seqera Containers in the container directive.

  1. In a terminal window, create a new directory for the Nextflow pipeline.

  2. Create a nextflow.config file with the following contents:

    docker {
      enabled = true
    }

  3. Create a main.nf file with the following contents:

    process SAMTOOLS {
      container '<CONTAINER_URI>'
      debug true
      """
      samtools --version-only
      """
    }
    workflow {
      SAMTOOLS()
    }

    Replace <CONTAINER_URI> with the container URI that you received from Seqera Containers in the previous section. For example:

    • community.wave.seqera.io/library/samtools:1.20--b5dfbd93de237464 for linux/amd64.
    • community.wave.seqera.io/library/samtools:1.20--497854c5df637867 for linux/arm64.

Run the Nextflow pipeline​

To confirm that the samtools command is available from your pipeline, run the following command:

nextflow run main.nf

If successful, you will see output similar to the following:

N E X T F L O W   ~  version 24.04.4

Launching `main.nf` [furious_carlsson] DSL2 - revision: 04817f962f

executor >  local (1)
[2f/d2ccc7] process > SAMTOOLS [100%] 1 of 1 ✔
1.20+htslib-1.20

Next steps​

Visit Seqera Containers to learn more about Seqera's container solutions.