#!/usr/bin/env python
# filename: antibody_ngs_pipeline

from antibody_ngs_pipeline import config
from antibody_ngs_pipeline import horseshoe as scripps


if __name__ == '__main__':
    #Preprocessing the data if specified
    if config.ARGS.fastqc or config.ARGS.adapter_fasta != None:
        scripps.preprocess(config.ABSTAR_ARGS, config.ARGS)

    #Run Abstar On Basespace Project
    scripps.run_abstar(config.ABSTAR_ARGS, config.PROJECT)

    #Import the data to a MongoDB
    scripps.run_mongo_import(config.MONGO_ARGS)

    #To Do: Correct data by UIDs
    
    #To Do: Import the data to S3
    #scripps.run_s3_import(config.S3_ARGS)