Awscli can't find libz share object file when running nextflow workflow on AWS Batch

[emiller (Edmund Miller)]

Libz.so missing for AWS CLI in AWS batch tasks

As a closure for this - we did some analysis by using ldd and it seems the aws v2 CLI does not locate the libz.so.1 that is distributed with its binary. And on a (slim) docker image with no existing libz - the AWS CLI then fails. We have fixed this by manually adding a LD_LIBRARY_PATH in nextflow config that explicitly points the directory of the mounted AWS CLI.

This might be the answer!