BinFlow/nextflow.saekho.config at main · dimi-lab/BinFlow · GitHub

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/*
Set default parameters

Any parameters provided by the user with a -params-file or
with -- command-line arguments will override the values
defined below.
*/

profiles {
  slurm {
    includeConfig 'conf/slurm.config'
  }
  local {
    includeConfig 'conf/local.config'
  }
}


params {
    help = false

    // Column name in the input spreadsheet that contains the concatinated list of marker labels.
    singleLabelColumn = "Classification"
    keptContextColumns = ["Image", " Centroid X µm", "Centroid Y µm"]
    singleLabelDelimiter = "|"
    //qupath_object_type = "DetectionObject"
    qupath_object_type = "CellObject"

    nucleus_marker = "NA2"

    use_boxcox_transformation = true
    transformation_group_by_column = "Image"

    // Rough estimator of bottom percentile belonging to negative labelling (1-99 percentile)
    huerustic_negative_percentile = 12
    huerustic_negative_n_cells = 8
    huerustic_negative_add_only_missing = "True"

    hasFOV = false

}

// Needed to modify lables from original to match marker quant prefix
// sed -i 's/CD8+/CD8a+/g' /.../QuantBinary/*
// sed -i 's/ HLA_DR+/ HLA-DR+/g' /.../QuantBinary/*