@<1554638160548335616:profile|AverageSealion33> looks like hydra pulls the config relative to the scripts directory, and not the current working directory. The pipeline controller actually creates a temp file in /tmp when it pulls the step, so the script's directory will be /tmp and when searching for ../data , hydra will search in / . The .git likely caused your repository to be pulled, so your repo structure was created in /tmp , which caused the step to run correctly.
What you could do is this to make hydra search via cwd:

from clearml import Task
import os
import hydra


@hydra.main(config_path=os.path.join(os.getcwd(), "../configs/preprocessing/"), config_name="config", version_base=None)
def main(cfg):
    Task.init("hydra", "hydra")
    print(cfg)


if __name__ == "__main__":
    main()