How to run nf-core rnaseq pipeline on AWS


I forked the nfcore rnaseq pipeline from github ( GitHub - nf-core/rnaseq: RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control. ), to add some steps for my analysis.

Then i tried to create a aws profile inside the nextflow.config, as folows:

    aws {
        docker.enabled = true
        params {
            config_profile_description = 'AWSBATCH Cloud Profile'
            config_profile_url = ''
            awsregion = 'eu-west-3'

        timeline {
            overwrite = true
        report {
            overwrite = true
        trace {
            overwrite = true
        dag {
            overwrite = true

        process.executor = 'awsbatch'
        process.queue = myjobqueue
        aws.cliPath = '/usr/local/bin/aws'
        aws.region = params.awsregion

But I always have this error, no matter what I modify on my aws profile:

Command error:
  bash: aws: command not found
  bash: line 1: aws: command not found

How to simply run rnaseq nfcore pipeline on aws ?

Thank you

In terms of configuration to run a nf-core pipeline on AWS Batch, you can read here what’s needed.

As for your error, you’re missing a scope. It’s aws.batch.cliPath, not aws.cliPath. You can read more about it here.