I am wondering if there is a way - or plans for a future feature - to override the entrypoint when running a docker container from a CWL Command Line Tool. In other words, is there a way to add the
--entrypoint argument in the
docker run command?
Thank you very much.
Here is what the CWL standards have to say about software container entrypoints
Use of implicit ENTRYPOINT or CMD are discouraged due to reproducibility concerns of the implicit hidden execution point (For further discussion, see https://doi.org/10.12688/f1000research.15140.1). Portable CommandLineTool wrappers in which use of a container is optional must not rely on ENTRYPOINT or CMD. CommandLineTools which do rely on ENTRYPOINT or CMD must list
DockerRequirement in the
Given that this practice is discouraged, I’m not surprised that I can’t find any proposal to override entrypoints, no
Sorry! I recommend changing your docker container to not use