/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    Python-only profile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    Use with a software profile, for example:

        nextflow run nf-core/scdownstream -profile docker,python_only --input samplesheet.csv --outdir results

    Replaces R-based default tools with Python implementations:

        ambient_correction  decontX (R)      → scAR (scvi-tools)
        doublet_detection   scDblFinder (R)  → Scrublet (scanpy)
        feature_selection   deviance (R)     → HVGs (scanpy)
        normalization       scran (R)        → log1p (scanpy)

    Default integration (scVI), clustering (scanpy), filtering (scanpy), and optional
    CellTypist annotation are already Python-based and unchanged.

    scAR requires both filtered and unfiltered matrices per sample (same as SoupX).
    For filtered-only input, set --ambient_correction none or disable ambient
    correction per sample in the samplesheet.

    Opt-in R tools (SoupX, SingleR/celldex, Seurat integration) are not overridden;
    avoid combining this profile with those parameters.
*/

params {
    config_profile_name        = 'Python only'
    config_profile_description = 'Use Python-based tools instead of R-based defaults (scAR, Scrublet, scanpy HVGs)'

    ambient_correction         = 'scar'
    doublet_detection          = 'scrublet'
    feature_selection          = 'hvgs'
    normalization_method       = 'log1p'
}
