Override Docker entrypoint in Command Line Tool

CWL Questions
1

Hello,

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.

2

Welcome @camilovelezr

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 requirements section.

From https://www.commonwl.org/v1.2/CommandLineTool.html#DockerRequirement

Given that this practice is discouraged, I’m not surprised that I can’t find any proposal to override entrypoints, no

https://github.com/search?q=org%3Acommon-workflow-language+entrypoint&state=open&type=Issues

Sorry! I recommend changing your docker container to not use ENTRYPOINT.

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