Using AWS Batch with a pre-defined Job Definition

[decibel-tom]

I'm working on a nextflow pipeline to utilize AWS Batch. I have created the required AWS Batch resources on my AWS account (compute environment, job queue, and job definition). It seems like I can easily use the job queue in Nextflow with the process.queue directive, but I can't use my pre-defined job definition. Nextflow keeps creating a new version of its own job definition, which does not have all the capabilities I need. Is there a way to override this to use my job definition?

I've tried using the syntax recommended here, but it still doesn't seem to be working properly. My processes also use a docker container, so I don't know if I can use the "process.container" directive twice in the same block, or if the latter overwrites the job-definition container?

[pditommaso]

Please provide the corresponding .nextflow.log file

[decibel-tom]

I changed my workflow slightly to put more information in a launch template for EC2 to be used by the job queue, omitting my need for a separate job definition. I can now use the job definition created by Nextflow rather than worrying about using my own. I unhelpfully no longer have access to that .log file