{
  "scaleTransformProcessingSteps": [
    {
      "name": ["flowframe_read"],
      "FUN": ["readSampleFiles"],
      "ARGS": {
        "whichSamples": ["all"],
        "truncate_max_range": [false],
        "min.limit": null
      }
    },
    {
      "name": ["remove_margins"],
      "FUN": ["removeMarginsPeacoQC"],
      "ARGS": []
    },
    {
      "name": ["compensate"],
      "FUN": ["compensateFromMatrix"],
      "ARGS": {
        "matrixSource": ["fcs"]
      }
    },
    {
      "name": ["flowframe_aggregate"],
      "FUN": ["aggregateAndSample"],
      "ARGS": {
        "nTotalEvents": [10000],
        "seed": [0]
      }
    },
    {
      "name": ["scale_transform_estimate"],
      "FUN": ["estimateScaleTransforms"],
      "ARGS": {
        "fluoMethod": ["estimateLogicle"],
        "scatterMethod": ["linearQuantile"],
        "scatterRefMarker": ["BV785 - CD3"]
      }
    }
  ],
  "flowFramesPreProcessingSteps": [
    {
      "name": ["flowframe_read"],
      "FUN": ["readSampleFiles"],
      "ARGS": {
        "truncate_max_range": [false],
        "min.limit": null
      }
    },
    {
      "name": ["remove_margins"],
      "FUN": ["removeMarginsPeacoQC"],
      "ARGS": []
    },
    {
      "name": ["compensate"],
      "FUN": ["compensateFromMatrix"],
      "ARGS": {
        "matrixSource": ["fcs"]
      }
    },
    {
      "name": ["remove_doublets"],
      "FUN": ["removeDoubletsCytoPipeline"],
      "ARGS": {
        "areaChannels": ["FSC-A", "SSC-A"],
        "heightChannels": ["FSC-H", "SSC-H"],
        "nmads": [3, 5]
      }
    },
    {
      "name": ["remove_debris"],
      "FUN": ["removeDebrisManualGate"],
      "ARGS": {
        "FSCChannel": ["FSC-A"],
        "SSCChannel": ["SSC-A"],
        "gateData": [73615.0, 110174.0, 213000.0, 201000.0, 126000.0, 47679.0, 260500.0, 260500.0, 113000.0, 35000.0]
      }
    },
    {
      "name": ["remove_dead_cells"],
      "FUN": ["removeDeadCellsManualGate"],
      "ARGS": {
		"FSCChannel": ["FSC-A"], 
        "LDMarker": ["L/D Aqua - Viability"],
		"gateData": [0.0, 0.0, 250000.0, 250000.0, 0.0, 650.0, 650.0, 0.0]
      }
    },
    {
      "name": ["perform_QC"],
      "FUN": ["qualityControlPeacoQC"],
      "ARGS": {
        "preTransform": [true],
        "min_cells": [150],
        "max_bins": [500],
        "step": [500],
        "MAD": [6],
        "IT_limit": [0.55],
        "force_IT": [150],
        "peak_removal": [0.3333],
        "min_nr_bins_peakdetection": [10]
      }
    },
    {
      "name": ["transform"],
      "FUN": ["applyScaleTransforms"],
      "ARGS": []
    }
  ]
}
