def load_pipeline_templates(self, template_dir):
pl_glob=os.path.join(template_dir, 'pipeline', '*.syml')
from Rnaseq import Pipeline # stupid class method
for pl_temp in glob.iglob(pl_glob):
pipeline_name=re.sub('\.\w+$','',os.path.basename(pl_temp))
pipeline=Pipeline(name=pipeline_name, path=pl_temp)
pipeline.store_db()
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
def test_context(self):
pipeline_file=os.path.join(dir, 't', 'fixtures', 'pipelines', 'simple_bowtie_p.yml')
pipeline=Pipeline(pipeline_file) # calls pipeline.load
inputs_file=os.path.join(dir, 't', 'fixtures', 'data', 'paired1.yml')
paired1=Inputs.load(inputs_file)[0]
context=pipeline.make_context(paired1)
self.assertEqual(context.step('Header').inputs, paired1.files)
self.assertEqual(context.step('Link').inputs, pipeline.step_named('Header').outputs())
self.assertEqual(context.step('Bowtie').inputs, pipeline.step_named('Link').outputs())
self.assertEqual(context.step('Footer').inputs, pipeline.step_named('Bowtie').outputs())
