README.md

scxa-tertiary-workflow

Tertiary component for SCXA workflows

How to run workflow for tertiary analysis

Prepare data

bash scripts/data_prep.sh <EXP-ID> [output path]

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.