snakefile.master

#----------------------------------------------------
#  Setup
#----------------------------------------------------


import sys
# import custom functions 
sys.path.insert(0, Path(workflow.basedir).parent.as_posix())
import Scripts.Functions.functions as func


# Define paths to different Snakefiles
pipelines = {
    "annotate": f"{workflow.basedir}/snakefile.annotate",
    "benchmark": f"{workflow.basedir}/snakefile.benchmark",
    "pretrain": f"{workflow.basedir}/snakefile.pretrain"
}


# Get the mode from the config
mode = config["mode"]

if mode not in pipelines:
    print(f"Error: Invalid mode '{mode}' specified.")
    sys.exit(1)

if mode == "benchmark":
  # In the benchmarking the finish output should be in the reference directory
  func.set_benchmark_directory(config,mode = 'benchmarking')

  def output_all_function():
    return [
        f"{output_dir_benchmark}/{reference}/benchmark.finished.succesfully.txt"
        for reference in config['references'].keys()
        for output_dir_benchmark in [config["references"][reference]["output_dir_benchmark"]]
    ]
  file_output = output_all_function()
else:
  file_output = config['output_dir'] + f"/{mode}.finished.succesfully.txt"


rule all:
  input:
    file_output
  
#rule all:
#  input:
#    config['output_dir'] + f"/{mode}.finished.succesfully.txt"

# Include the selected Snakefile
include: pipelines[mode]