Can anyone share the instructions for awsbatch?

Personally I don't experience running stuff in awsbatch, but I understand correctly, using

-profile awsbatch

should be enough. Are you using 5.4.2? We had a bug with the publishing of BUSCO output files that caused conflicts on S3. Are you seeing some specific error(s)?

Thanks for your reply. Actually, there is no awsbatch profile in 5.4.2, so I had to setup my own. MAG did't publish output files to s3 using profile test, even though all jobs are completed successfully. It is strange that there is no error in the log.

The awsbatch profile comes from the centralized nf-core configs, not from the mag repository: https://github.com/nf-core/configs/blob/master/conf/awsbatch.config. It should be fetched automatically at runtime. Since this seems more related to the AWS Batch / Nextflow setup, you may get better help in Nextflow’s infrastructure-aws. You will find people with more experience there.

Thanks