Nextflow script with both 'local' and 'awsbatch' executor

I have a Nextflow pipeline executed in AWS Batch. Recently, I tried to add a process that uploads files from local machine to S3 bucket so I don't have to upload files manually before each run. I wrote a python script that handles the upload and I wrapped it into a Nextflow process. Since I am uploading from a local machine, I want the upload process with
executor 'local'

This requires a Fusion filesystem enabled in order to have a Work Dir in S3. But when I enable the Fusion filesystem I don't have access to my local filesystem. In my understanding, when Fusion filesystem is enabled, the task runs in Wave container without access to host filesystem. Does anyone have experience with running Nextflow with FusionFS enabled and how to access host filesystem? Thanks!

I don't think you need to manage a hybrid workload here. Pipeline inputs can be stored either locally or in an S3 bucket. If your files are stored locally and you specify a working directory in S3, Nextflow will already try to upload them into the staging area for you. For example, if you specify your working directory in S3 using -work-dir 's3://mybucket/work', Nextflow will try to stage the input files under s3://mybucket/work/stage-<session-uuid>. Once the files are in the staging area, Nextflow can then begin to submit jobs that require them.

Note that a Fusion file system is not strictly required to have your working directory in S3. Nextflow includes support for S3. Either include your AWS access and secret keys in your pipeline configuration or use an IAM role to allow your EC2 instances full access to S3 storage.