# How to run nf-core rnaseq pipeline on AWS

**URL:** <https://community.seqera.io/t/how-to-run-nf-core-rnaseq-pipeline-on-aws/809>\
**Category:** Ask for help\
**Created:** [June 3, 2024, 2:15pm UTC](https://community.seqera.io/t/how-to-run-nf-core-rnaseq-pipeline-on-aws/809 "2024-06-03T14:15:24Z")\
**Posts on this page:** 2\
**Page:** 1

<div class="post-metadata">

**Author:** ![alyseal](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/alyseal/32/730_2.png) [@alyseal](https://community.seqera.io/u/alyseal)\
**Post date:** [June 3, 2024, 2:15pm UTC](https://community.seqera.io/t/how-to-run-nf-core-rnaseq-pipeline-on-aws/809/1 "2024-06-03T14:15:24Z")

</div>

Hello,

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.](https://github.com/nf-core/rnaseq) ), to add some steps for my analysis.

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

```auto
    aws {
        docker.enabled = true
        params {
            config_profile_description = 'AWSBATCH Cloud Profile'
            config_profile_url = 'https://aws.amazon.com/batch/'
            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:

```auto
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

---

<div class="post-metadata">

**Author:** ![mribeirodantas](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/mribeirodantas/32/235_2.png) [@mribeirodantas](https://community.seqera.io/u/mribeirodantas)\
**Post date:** [June 3, 2024, 2:50pm UTC](https://community.seqera.io/t/how-to-run-nf-core-rnaseq-pipeline-on-aws/809/2 "2024-06-03T14:50:43Z")

</div>

In terms of configuration to run a nf-core pipeline on AWS Batch, you can read [here](https://github.com/nf-core/configs/blob/52edad2f413ca274eb29c98e40e709756963cd5f/docs/awsbatch.md) 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](https://www.nextflow.io/docs/latest/config.html#scope-aws).