Nextflow and Wave

You can provision containers with Wave directly from your Nextflow pipelines.

Prerequisites

• You have an account with a container registry, such as DockerHub, and an access token that provides write access to your container repository.
• You have a Seqera account to log into Platform.
• You have either Docker Desktop or Podman installed locally.
• You have Nextflow 23.10.x or newer installed locally.

In this guide, you'll build a container from a Nextflow module and freeze that package in your private container repository.

Create your Seqera access token

1. Log in to Seqera.

2. From your personal workspace: Go to the user menu and select Settings > Your tokens.

3. Select Add token.

4. Enter a unique name for your token, then select Add.

5. Copy and store your token securely.

   caution

   The access token is displayed only once. Save the token value before you close the Personal Access Token window.

6. In a terminal window, assign your access token to the TOWER_ACCESS_TOKEN environment variable:

   export TOWER_ACCESS_TOKEN=<token_token>

Add your container registry credentials to Seqera

When freezing a container to the build repository that you specify, Wave uses Seqera to obtain your registry access credentials. If you use Docker as your container registry, complete the following steps:

To create your access token in Docker Hub:

1. Log in to Docker Hub.
2. Select your username in the top right corner and select Account Settings.
3. Select Security > New Access Token.
4. Enter a token description. Select Access permissions > Read-only, then select Generate.
5. Copy and save the generated access token (this is only displayed once).

To add your credentials to Seqera:

1. Add your credentials to your organization or personal workspace:

   • From an organization workspace: Go to Credentials > Add Credentials.
   • From your personal workspace: From the user menu, go to Your credentials > Add credentials.

2. Complete the following fields:

   • Name: Specify a unique name for the credentials using alphanumeric characters, dashes, or underscores. For example, my-registry-creds.
   • Provider: Select Container registry.
   • User name: Specify your Docker username. For example, user1.
   • Password: Specify your personal access token (PAT). For example, 1fcd02dc-...215bc3f3.
   • Registry server: Specify the container registry hostname, excluding the protocol. For example, docker.io.

3. Select Add. The new credential will be listed under the Credentials tab.

Seqera supports other container registries, such as GitHub and Quay.io.

Create a Nextflow pipeline that uses Wave

Nextflow can use Wave to seamlessly build a container directly from a Dockerfile in your pipeline.

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
   }
   
   wave {
     build.repository = '<repo_uri>'
     wave.freeze = true
   }
   
   tower {
     accessToken = "$TOWER_ACCESS_TOKEN"
   }

   The <repo_uri> must be substituted with your private container repository.

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

   include { HELLO } from './modules/gamma'
   
   workflow {
     HELLO()
   }

4. Create a directory for the module:

   mkdir -p modules/gamma

5. Create the modules/gamma/main.nf file for the module:

   process HELLO {
     debug true
   
     """
     cowsay Hello!
     """
   }

6. Create the modules/gamma/Dockerfile file for the module:

   FROM alpine
   
   RUN apk update && apk add bash cowsay \
     --update-cache \
     --repository https://alpine.global.ssl.fastly.net/alpine/edge/community \
     --repository https://alpine.global.ssl.fastly.net/alpine/edge/main \
     --repository https://dl-3.alpinelinux.org/alpine/edge/testing
   
   RUN echo hello

Run the Nextflow pipeline

To run the pipeline, and initiate the Wave container build, enter the following command:

nextflow run wave.nf -with-wave

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

Launching `wave.nf` [naughty_wiles] DSL2 - revision: 3756d705d9

executor >  local (1)
[c1/6d7d9d] HELLO | 1 of 1 ✔
 ________
< Hello! >
 --------
        \   ^__^
         \  (oo)\_______
            (__)\       )\/\
                ||----w |
                ||     ||