config

This folder contains additional configuration files for running the scpca-nf workflow, as described below. To use a configuration file, it must be referenced in the main configuration file (i.e., nextflow.config) using includeConfig.

• containers.config: Docker containers used by scpca-nf workflow processes
• process_base.config: default resource settings for scpca-nf workflow processes
• profile_awsbatch.config: legacy AWS Batch configuration for Data Lab users
• profile_awsbatch_auto.config: AWS Batch configuration with auto-scaling disks for Data Lab users
• profile_ccdl.config: file locations for Data Lab users only, as described in internal-instructions.md
• profile_stub.config: file locations used for testing scpca-nf workflow logic, as described in internal-instructions.md
• profile_example.config: file locations for re-generating example scpca-nf workflow output, as described in internal-instructions.md