Issues regarding python boto3 and nextflow syntax :(

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Jyotsana Mehra

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Sep 27, 2022, 2:04:41 PM9/27/22

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Hi Everyone, my doubt is regarding Nextflow and boto3 python AWS services. I have prepared one boto3 package based python script which will create an instance for me in AWS using an AMI (which do have nextflow requirement packages) and now in that instance I want to run my nextflow syntax.

Assume my basic syntax is -

nextflow run nf-core/sarek -r 3.0.2 -profile test --outdir <OUTDIR>

Here outdir is my s3://bucket path where I want to save my results. But, nextflow script is not running. I am using python boto3 "UserData" argument and in quotes writing nextflow script. I tested this using shell script it is working, but not nextflow syntax.