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Nextflow and Seqera Containers

You can provision containers that include conda packages through Seqera Containers and use them directly in your Nextflow pipelines.

Prerequisites

  • You have either Docker Desktop or Podman installed locally.
  • You have Nextflow 23.10.x or newer installed locally.
  • Use Singularity 4.x or newer to run the Singularity containers.

In this guide, you'll request a containerized Conda package from Seqera Containers.

Request a conda package as a Seqera Container​

  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 the durable 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()
    }

    Substitute <container_uri> for the container URI that you received from Seqera Containers in the previous section. e.g.

    • 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

The output from a successful execution is displayed in the following example:

 N E X T F L O W   ~  version 24.04.4

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

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