@Ken Brewer Sorry I haven't been able to test that PR yet. I wanted to mention that when I use the CellProfiler CLI in my internal function/TBD package called CP_Parallel, I have used the following command when using a LoadData CSV:

# set command up to use for a loaddata csv
            command = [
                "cellprofiler",
                "-c",
                "-r",
                "-p",
                path_to_pipeline,
                "-o",
                path_to_output,
                "--data-file",
                path_to_loaddata,
            ]

I don't ever reference the image directory in this case because as @Erin Weisbart says, it uses the

PathName_CHANNEL

to find the images. From my understanding, you shouldn't need to specify --image-directory or --i flag in this instance. Hope this helps, as I see you are calling both data-file and image-directory.

Unfortunately we can't use the

PathName_Channel

approach when using Nextflow. Because of the way Nextflow stages data for each task execution into individual task directories, you never know the full path to the images ahead of time. Instead you need to use paths relative to the current working directory.