Running Nextflow pipeline on GCP

Google genomic API allows auto scale for computational resources by creating and closing VMs automatically. We have a dedicated google project caendr which using Google genomic APT for all the nextflow pipelines in our lab. To access it, you should provide your gmail accout to Erik and ask Erik give you a project owner role for caendr. I already preset the project to enable running Nextflow pipelines using Google genomic API. See below for more details.

Enable API

Go the the main page of google cloud platform. In the Produck & Services menu, click APIs & Services, and then click Enable APIs and Services. The following APIs should be enabled to run nextflow pipeline on GCP.

  • Genomics API
  • Cloud Life Sciences API
  • Compute Engine API
  • Google Container Registry API

Create service account

Go to the IAM & admin, find the Service accounts. Click CREATE SERVICE ACCOUNT to create a new service accounts. Note this service accounts must have a project owner role to run Nextflow pipelines. The service account I created here is called nextflowRUN.

You don't need to do the above processes when you use GCP. But you have to do all the following processes to make sure you have the right permissions to caendr.

Generate credential for the service account

After you get the access to caendr, go to the API & Services. Click the Create credentials button, select Service account key. And choose nextflowRUN to generate a JSON file, which is a privite key file for using nextflowRUN. Download the file and save it in a safe place. Finally, define the GOOGLE_APPLICATION_CREDENTIALS variable in .bash_profile with the directory of the JSON file. Which should looks like the example.

export GOOGLE_APPLICATION_CREDENTIALS=$HOME/google_creds/caendr-2cae6210c8d1.json

Nextflow version and mode

Only the version of 19.07.0 or higher of Nextflow are compatible with GCP. And also, the Nextflow should have a google mode. You can define the version and mode in .bash_profile.

export NXF_VER=19.07.0
export NXF_MODE=google

Then, run the following code to update or install Nextflow.

curl | bash

Configure Nextflow for GCP

To run Nextflow pipelines on GCP, you need to build docker images for them. Check the docker file repo of our lab for more information.

The google genomic API has its own executor called google-pipelines, you need to define the executor variable with google-pipelines in the nextflow.config file. Here is the example for concordance-nf.

docker {

    enabled = true


process {
    executor = 'google-pipelines'

    withLabel: bam_coverage {
        container = 'faithman/bam_toolbox:latest'

    container = 'faithman/concordance:latest'
    machineType = 'n1-standard-4'

google {
    project = 'caendr'
    zone = 'us-central1-a'

cloud {
    preemptible = true

executor {
    queueSize = 500


The file system of google buckets is not like S3 that can read/write directly by most softwares. You have to use gsutil tool to interact with google buckets to read/write files in most situations. Nextflow has built-in functions to interact with google buckets, but you still can not read/write files directly in your script. All the files have to be read and write via channels in Nextflow!