01 run with cli

1. Use Seqera Platform to capture and monitor Nextflow jobs launched from the CLI

We'll start by using the Nextflow CLI to launch a pipeline and monitor it in Seqera Platform. Start by logging into the Seqera Platform.

Nextflow Tower

Seqera Platform was previously known as Nextflow Tower. You'll still see references to the previous name in environment variable and cli option names.

1.1. Set up your Seqera Platform token by exporting it to your environment

Follow these steps to set up your token:

1. Create a new token by clicking on the Settings drop-down menu:

   

2. Name your token:

   

3. Save your token safely:

   

   Note

   Leave this browser tab open as we will need the token once more to store it as a Nextflow secret.

4. To make your token available to the Nextflow CLI, export it on the command line:

   Open a terminal and type:

    export TOWER_ACCESS_TOKEN=eyxxxxxxxxxxxxxxxQ1ZTE=
   

   Where eyxxxxxxxxxxxxxxxQ1ZTE= is the token you have just created.

1.2. Run Nextflow cli with Seqera Platform visualizing and capturing logs

Run your Nextflow workflows as usual with the addition of the -with-tower command:

nextflow run nextflow-io/hello -with-tower

You will see output similar to the following:

Output

 N E X T F L O W   ~  version 24.04.4

Launching `https://github.com/nextflow-io/hello` [evil_engelbart] DSL2 - revision: afff16a9b4 [master]

Downloading plugin nf-tower@1.9.1
Monitor the execution with Seqera Platform using this URL: https://cloud.seqera.io/user/kenbrewer/watch/5Gs0qqV9Y9rguE
executor >  local (4)
[80/810411] process > sayHello (1) [100%] 4 of 4 ✔
Ciao world!

Bonjour world!

Hola world!

Hello world!

Use ++ctrl+click++ or ++cmd+click++ on the link to open it in your browser. You'll see the Seqera Platform interface with the job finished and the logs captured.

You will see and be able to monitor your Nextflow jobs in Seqera Platform.

1.3. Set up Seqera Platform in Nextflow configuration

Doing that token setup regularly can get bit tedious, but the same setup can be applied in configuration applied to Nexflow configuration so that it does not need to be set each time. This can be the nextflow.config file of a specific project, or the global file located at $HOME/.nextflow/config, which will apply to all your runs.

Before we set the configuration, we need to permanently store the token in Nextflow using a Nextflow secret:

nextflow secrets set tower_access_token "eyxxxxxxxxxxxxxxxQ1ZTE="

We want to configure Nextflow to use Seqera Platform by default across all our pipelines, so we will open the global Nextflow configuration file ($HOME/.nextflow/config) for editing:

code $HOME/.nextflow/config

Add the following configuration to the file:

$HOME/.nextflow/config

tower {
    enabled = true
    accessToken = secrets.tower_access_token
    workspaceId = secrets.tower_workspace_id
    endpoint = "https://api.cloud.seqera.io"
}

!!! hint "Workspace ID and Endpoint`

We haven't set `secrets.tower_workspace_id` yet, and so Nextflow will fill in an empty string for this value.
This will default to the user's workspace in Seqera Platform which is what we want for now.

The `endpoint` is the URL of the Seqera Platform API.
If your institution is running a private instance of Seqera Platform, you will want to change this to the appropriate URL.

Run your Nextflow workflows as usual:

nextflow run nextflow-io/hello

You will see the following output:

Output

 N E X T F L O W   ~  version 24.04.4

Launching `https://github.com/nextflow-io/hello` [fabulous_euclid] DSL2 - revision: afff16a9b4 [master]

Monitor the execution with Seqera Platform using this URL: https://cloud.seqera.io/user/kenbrewer/watch/KYjRktIlOuxrh
executor >  local (4)
[71/eaa915] process > sayHello (3) [100%] 4 of 4 ✔
Ciao world!

Bonjour world!

Hola world!

Hello world!

Note that we are logging to Seqera Platform even though we did not use the -with-tower command!

1.4. Use Seqera Platform to explore the resolved configuration of a Nextflow pipeline

Click on the link provided in the output to open the Seqera Platform for your run, then click on the Configuration tab. If you ran your pipeline from the hello_nextflow directory, you'll see something like this:

Notice that configuration for our pipeline run is being run pulled from three separate files:

• /home/gitpod/.nextflow/config - This is the global configuration file we just added.
• /home/gitpod/.nextflow/assets/nextflow-io/hello/nextflow.config - This is the nextflow.config file from the nextflow-io/hello repository.
• /workspace/gitpod/nf-training/hello-nextflow/nextflow.config - This is the nextflow.config file from our current working directory.

Nextflow resolves these configurations at runtime with a specific order of precedence. The general rule, however, is that more specific configurations override less specific ones, and config/params specified on the CLI will override defaults in the config files.

Helpfully, Seqera Platform shows us the final output of this configuration resolution process which can be very useful for debugging!

Takeaway

You have learned how to:

• Set up your Seqera Platform token by exporting it to your environment.
• Run Nextflow CLI with Seqera Platform visualizing and capturing logs.
• Set up Seqera Platform logging by default.
• Use Seqera Platform to explore the resolved configuration of a Nextflow pipeline.

What's next?

Learn how to launch Nextflow pipelines from Seqera Platform using the Launchpad feature.