iss-nf/nextflow.config at main · BioImageTools/iss-nf · GitHub

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def INPUTDIR = "/path/to/your/dataset"

params {
    PoSTcode = true
    inputRefImagePath = INPUTDIR + "anchor_nuclei.tif*"
    inputMovImagesLearnPath = INPUTDIR + "r*_DAPI.tif*"
    movingImagesApplyPath = INPUTDIR + "r*_*.tif*"
    inputUntransformedImagesPath = INPUTDIR + "anchor_*.tif*"
    elastix_parameter_files =  "/$baseDir/parameter_files/elastix_parameters_2D_*.txt"
    ExpMetaJSON = INPUTDIR + "experiment_metadata.json"
    CodeJSON = INPUTDIR + "codebook.json"
    filt_radius = "5"
    rescale_factor = "5"
}

profiles {

    conda {
        conda.enabled          = true
        docker.enabled         = false
        singularity.enabled    = false
        podman.enabled         = false
        shifter.enabled        = false
        charliecloud.enabled   = false
        apptainer.enabled      = false
    }
    mamba {
        conda.enabled          = true
        conda.useMamba         = true
        docker.enabled         = false
        singularity.enabled    = false
        podman.enabled         = false
        shifter.enabled        = false
        charliecloud.enabled   = false
        apptainer.enabled      = false
    }
    docker {
        docker.enabled         = true
        conda.enabled          = false
        singularity.enabled    = false
        podman.enabled         = false
        shifter.enabled        = false
        charliecloud.enabled   = false
        apptainer.enabled      = false
        docker.runOptions      = '--entrypoint ""'
    }
    singularity {
        singularity.enabled    = true
        singularity.autoMounts = true
        conda.enabled          = false
        docker.enabled         = false
        podman.enabled         = false
        shifter.enabled        = false
        charliecloud.enabled   = false
        apptainer.enabled      = false
    }
    apptainer {
        apptainer.enabled       = true
        apptainer.autoMounts    = true
        conda.enabled           = false
        docker.enabled          = false
        singularity.enabled     = false
        podman.enabled          = false
        shifter.enabled         = false
        charliecloud.enabled    = false
    }
}
// Load modules.config for DSL2 module specific options
includeConfig 'conf/slurm.config'