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