def test_basic(self):
pipeline_file=os.path.join(dir, 't', 'fixtures', 'pipelines', 'simple_bowtie_p.yml')
pipeline=Pipeline(pipeline_file)
inputs_file=os.path.join(dir, 't', 'fixtures', 'data', 'paired1.yml')
paired1=Inputs.load(inputs_file)[0]
sh=pipeline.sh_script(paired1)
print sh
