#!/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.quality_trim or config.ARGS.adapter_fasta != None:
        #Run Abstar On Basespace Project with preprocessing
        scripps.run_abstar(config.ABSTAR_ARGS, config.PROJECT, config.ARGS, preprocessing=True)
    else:
        #Run Abstar On Basespace Project without preprocessing
        scripps.run_abstar(config.ABSTAR_ARGS, config.PROJECT, config.ARGS)

    #Import the data to a MongoDB
    scripps.run_mongo_import(config.MONGO_ARGS)
    
    #To Do: Import the data to S3
    #scripps.run_s3_import(config.S3_ARGS)