I was following along the steps described here to set up my AWS batch. The machine type is AWS Linux with compute environment having
AWSServiceRoleForBatch and ecsInstanceRole attached.
Anyways, I solved my original problem with help from @robsyme on a call. The path to my aws-cli was in /usr/local/bin in my nextflow config. This was mounting /usr/local/bin from the AMI and blocking whatever in my docker container /usr/local/bin (like the bigWigToBedGraph in my docker image)
I updated where my aws-cli was and pointed to a more inncoucrous path in my config and the pipeline ran just fine.