Run Nextflow CLI with Seqera Platform visualizing and capturing logs

Run Nextflow CLI with Seqera Platform visualizing and capturing logs#

Seqera platform#

The Seqera Platform is a collaborative environment where pipelines and analysis results can be launched, cataloged, monitored, organized, and shared with colleagues.

Seqera platform can help us by:

  1. giving researchers early access to pipelines and computational resources

  2. promoting effective collaboration,

  3. standardizing and accelerating the generation of results,

  4. ensuring compliance and security providing the framework for reliable and reproducible pipeline execution

  5. allowing us to optimize and reduce computing and storage costs

Run hello.nf script and follow the run in Seqera platform#

First you need to create an account and create an access token. Later you need to export the token to your system:

export TOWER_ACCESS_TOKEN=copyandpastetokenfromtheSqeraPlatformhere

Now get back to the directory where the hello.nf script is.

cd ../..

Lets’s run our first nextflow script in Seqera with the addition of the -with-tower command:

hello.nf capturing logs in Seqera platform#
nextflow run hello.nf -with-tower

If it run properly you should have got an URL like this one: Monitor the execution with Seqera Platform using this URL: <https://cloud.seqera.io/user/apca1/watch/1CexaaYrhJc2JE>. If you copy and paste that link in your browser you get a report of the workflow run with logs information (run information, cpus used, memory used, processes that succeded, processes that failed, etc…). This can be categorized as you desire and the runs can be shared among your collaborators. Pipelines can also be launched from the Platform.