run.config

process {
	withName: CELLPOSE {
		maxForks = 1
		clusterOptions = '-gpu "mode=shared:j_exclusive=no:num=1:gmem=2048"'
		// ext.args = "--flow_threshold 1.0 --cellprob_threshold -1.0"
	}

	withName: BIOINFOTONGLI_MICROALIGNER {
		storeDir = "output/registered_stacks/"
        memory = {50.Gb *task.attempt}
		queue="imaging"
	}

	withName: TO_SPATIALDATA {
        ext.args = "--feature_col 'Name' --expansion_in_pixels 80 --save_label_img True"
        memory = {40.Gb *task.attempt}
		queue = "imaging"
	}

	withName: BIOINFOTONGLI_TILEDSPOTIFLOW {
		memory = {20.Gb *task.attempt}
		clusterOptions = '-gpu "mode=shared:j_exclusive=no:num=1:gmem=2048"'
		maxForks = 1
	}

	withName: Spotiflow_merge_tiled_peaks {
		memory = {20.Gb *task.attempt}
		maxForks = 1
	}
}