Hm, I've been trying to test this behaviour locally, however it works for me even before this fix (tried both the natively-compiled version from master and the linux one from the latest release).
What I'm doing is to run the following command:

TOWER_API_ENDPOINT=http://localhost:8080 ./tw --insecure launch test-cli-ce-pre-post --post-run=../pre-run-sh

test-cli-ce-pre-post has both scripts defined in the CE, and I can see that the post-run is being overwritten by my argument

Also, I wasn't sure whether you meant that the scripts are defined when you add a pipeline, or when you launch it, so I tested the other scenario too, where I have the scripts defined in the CE, and then overwritten when adding the pipeline. Not providing parameters from the cli:

TOWER_API_ENDPOINT=http://localhost:8080 ./tw --insecure launch test-ce-pre-post-redefined

and it also worked correctly.

What am I missing?

Hey @tcrespog do we want to move this forward?

Hi, @weronikasosnowskaseqera. I realized that the nextflowConfig field has the same behaviour as preRunScript and postRunScript; however, nextflowConfig is not present among the class fields, so it requires an explicit update of the SDK. I was planning to do that, but had to address other matters.

Hey @tcrespog - I have a PR with another version bump of the tower-java-sdk to a version that would supersede the one in this PR.
Would that be safe to merge without this PR or is this one a prerequisite to be merged in first?
The changes in this one look backwards compatible to me, but double checking.

Would that be safe to merge without this PR or is this one a prerequisite to be merged in first?

Hi, @georgi-seqera. It is okay if you merge yours first. Thank you.

@tcrespog merge conflict seems easy but can you check if additional changes are required to move this PR forward?