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  • Users' Pipelines
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1. Connect AWS Integration

Open the following link to connect your AWS account automatically to Tracer. This will allow Tracer to monitor your AWS Batch jobs.—> Connect AWS

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2. Locate the EC2 LaunchTemplate UserData

In your CloudFormation template, find the UserData field within the Launch Template used by your AWS Batch compute environment.Reference example: CloudFormation Template
Resources >
  NextflowLaunchTemplate >
    Properties >
      LaunchTemplateData >
        UserData

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3. Update user_data_mime.sh

Update the user_data_mime.sh file to include your Tracer user ID. Navigate to the terraform directory and edit the file:
cd nextflow-test-pipelines/pipelines/aws-batch/rnaseq/terraform 
vim user_data_mime.sh
Important: Find line 120 in the file and update it with your user ID:
tracer init --token <your-token>
Note: If you need to change this later, you’ll need to refresh the infrastructure.See the exact line to update

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4. Setup infrastructure

Run the setup script to create the AWS infrastructure (VPC, S3, Batch, etc.):
cd nextflow-test-pipelines/pipelines/aws-batch/rnaseq
./run.sh setup
What this does: Creates VPC with public/private subnets, AWS Batch compute environment, S3 buckets for work directory and outputs, IAM roles and policies, security groups, and EC2 Instance Connect endpoint.
Alternative for Tracer AWS Account Users:
If you have access to Tracer’s AWS account, you can skip the infrastructure setup and run the pipeline directly with ./run.sh tracer run

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5. Run the RNA-seq pipeline

Execute the RNA-seq pipeline using the run script:
cd nextflow-test-pipelines/pipelines/aws-batch/rnaseq
./run.sh run

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