celltypist

Nextflow workflow for scRNAseq cell type annotation with CellTypist

Prerequisites:

• Nextflow
• Singularity

An example of the nextflow run script is in run.sh

Parameters:

• --samples TSV containing the sample IDs, paths to the normalized (scaled to counts per 10,000 and natural log with pseudocount) .h5ad count matrices and cell metadata (example: assets/input_examples/samplesheet.tsv)
• --model name of the CellTypist model to use
• --outdir name of the output directory

Outputs:

• annotate contains the count matrices with majority voted cell types in .h5ad files, cell type distributions, UMAPs, and CellTypist outputs
• celltype_concordance contains comparisons of annotated cell types to the metadata - cell type distributions and a confusion matrix