scxa-tertiary-workflow

Tertiary component for SCXA workflows

How to run workflow for tertiary analysis

Prepare data

To perform a tertiary analysis, all required datasets must be stored in a single directory, which should be specified using the --dir_path parameter.

Ensure the following files are present in the directory:

genes_metadata.tsv – Metadata information for genes genes.tsv – List of gene identifiers barcodes.tsv – Cell barcode identifiers matrix.mtx – Expression matrix in Matrix Market format cell_metadata.tsv – Metadata information for individual cells

Run for plate

nextflow run main.nf --slurm -resume --dir_path <EXP-ID with path> [--output_path <PATH>]  [--scanpy_scripts_container <container_id>] [--celltype_field <celltype_field>]

Run for droplet

nextflow run main.nf --slurm -resume --dir_path <EXP-ID with path> --technology droplet [--output_path <PATH>] [--scanpy_scripts_container <container_id>] [--celltype_field <celltype_field>]

If [--output_path <PATH>] is not specified results will be <EXP-ID with path>/results dir.