Updated CLI param parsing for Nextflow 24.10 #543

Job	Run time
setup	25s
ex002	8m 42s
ex001 (--viz, true)	10m 14s
ex001-by-step	15m 45s
ex001-singularity	14m 14s
ex001 (--start-at illumination --stop-at registration)	1m 56s
ex001 (--background)	10m 33s
ex001 (--background --background-method imagej-rolling-ball)	11m 34s
ex001 (--segmentation cypository --cypository-opts '--channel 10 --scalingFactor 2' --s3seg-opts ...	10m 0s
ex001 (--segmentation ilastik,mesmer)	4m 0s
ex001 (--segmentation cellpose --mcquant-opts '--masks *masks.tif')	6m 29s
	1h 33m 52s

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