Example of standard ruffus syntax

seperate_logic.py

from ruffus import transform, suffix, pipeline_run
from task_functions import run_bwa, sort_bam

@transform("*.fastq", suffix(".fastq"), ".bam")
def step1(infile, outfile);
    run_bwa(infile, outfile)
  
@transform(run_bwa, suffix(".bam"), ".sorted_bam")
def step2(infile, outfile):
    sort_bam(infile, outfile)
    
pipeline_run([step2], multithread=1)

simple.py

from ruffus import transform, suffix, pipeline_run

@transform("*.fastq", suffix(".fastq"), ".bam")                  
def run_bwa(input_file, output_file):
    print "Align DNA sequences in %s to a genome -> %s " % (input_file, output_file)
    # make dummy output file
    open(output_file, "w").close()    

@transform(run_bwa, suffix(".bam"), ".sorted_bam")
def sort_bam(input_file, output_file):
    print "Sort DNA sequences in %s -> %s " % (input_file, output_file)
    # make dummy output file
    open(output_file, "w").close()    
    
pipeline_run([sort_bam], multithread = 1)