Inputs to SherlockCell

Samplesheet file

The input parameters for SherlockCell are passed throught a samplesheet TSV file containing these fields:

dataset	adata_path	outdir	cell_origin	cell_type_key	sample_key	sample_type_key
datase_name	/path/to/adata.h5ad	/path/to/outdir	T-cells, Macrophages	cell_type	sample	sample_type

In the cell_origin field it is important to include Malignant cells if they are present in the annotation, so they are included as query for SwiftCNV. The sample_type_key is and adata.obs column where the type of sample has to be specified as 'tumor' or 'normal'.

Config file

Some parameters can also be set as default in the config file. Moreover, the parameters for SwiftCNV can be defined from here as well.

params {
    samplesheet = "/path/to/samplesheet.tsv"

    sample_key    = "sample"   
    cell_type_key = "cell_type"
    sample_type_key = "sample_type"

    swiftCNV {
        gene_annots  = "/path/to/gencode.v44.annotation.gtf.gz"
        HMM = false
        plot_cnv = true
        sex_chr = true
        cutoff = 0.1
    }
}