6.11 Reporting and graphical interface

Nextflow has an embedded function for reporting a number of informations about the resources needed by each job and the timing: you can get a nice html report with parameter -with-report:

nextflow run test5.nf -with-docker -bg -with-report > log

Nextflow Tower is an open source monitoring and managing platform for Nextflow workflows. There are two versions:

  • Open source for monitoring of single pipelines
  • Commercial one for workflow management, monitoring and resource optimisation.

We will show the open source one.

First of all you need to access the tower.nf website and doing the login using one of the methods.

We select the email for receiving the instructions and the token to be used for the pipeline.

So we check the email:

We then go on getting started and follow the instructions for exporting two environmental variables:

You can then generate your token here: https://tower.nf/tokens and copy paste in your pipeline using this snippet in the configuration file

tower {
  accessToken = '<YOUR TOKEN>'
  enabled = true

or exporting those environmental variables:

export TOWER_ACCESS_TOKEN=*******YOUR***TOKEN*****HERE*******
export NXF_VER=21.04.0

we then launch the pipeline:

nextflow run test5.nf -with-singularity -with-tower -bg > log

CAPSULE: Downloading dependency io.nextflow:nf-tower:jar:20.09.1-edge
CAPSULE: Downloading dependency org.codehaus.groovy:groovy-nio:jar:3.0.5
CAPSULE: Downloading dependency io.nextflow:nextflow:jar:20.09.1-edge
CAPSULE: Downloading dependency io.nextflow:nf-httpfs:jar:20.09.1-edge
CAPSULE: Downloading dependency org.codehaus.groovy:groovy-json:jar:3.0.5
CAPSULE: Downloading dependency org.codehaus.groovy:groovy:jar:3.0.5
CAPSULE: Downloading dependency io.nextflow:nf-amazon:jar:20.09.1-edge
CAPSULE: Downloading dependency org.codehaus.groovy:groovy-templates:jar:3.0.5
CAPSULE: Downloading dependency org.codehaus.groovy:groovy-xml:jar:3.0.5

We finally go to the tower website again:

And in the end when the pipeline is finished we can also receive a mail.