def setUp(self):
"""Set up a workflow.
"""
fqqf = FastqQualityFilter(
name="quality_filter", args={"-i": "fastq.fq", "-o": "qfastq.fq", "-Q": "33", "-q": "20", "-p": "90"}
)
fq2a = FastqToFasta(name="fastq_to_fasta", args={"-i": "qfastq.fq", "-o": "qfasta.fa"})
fq2a.add_dependencies(done=[fqqf])
self.wf = WorkFlow([fqqf, fq2a])
self.fqqf = fqqf
self.fq2a = fq2a
# data init
data_dir = '/home/karl/data/tfpipe/'
# build first job
job1 = galaxy.FastqToFasta(args={'-i':data_dir + 'rep2.fastq',
'-o': data_dir + 'rep2.fasta',
'-Q': '33'},
name='myfastq2a')
# build second job
job2 = galaxy.FastxClipper()
job2.add_argument('-i', data_dir + 'rep2.fasta')
job2.add_argument('-o', data_dir + 'newoutfile.fa')
job2.add_argument('-C')
job2.add_jobname("myFastxClipper")
job2.add_adapter_file('/home/karl/data/tfpipe/adapters')
job2.add_dependencies(done=[job1,])
job3 = CLI(cmd="ls -l")
# add jobs to workflow
wf = WorkFlow([job1, job2, job3], lsf=False)
wf.show()
class WorkFlowTest(unittest.TestCase):
"""Test functionality of workflow with sample jobs.
"""
def setUp(self):
"""Set up a workflow.
"""
fqqf = FastqQualityFilter(
name="quality_filter", args={"-i": "fastq.fq", "-o": "qfastq.fq", "-Q": "33", "-q": "20", "-p": "90"}
)
fq2a = FastqToFasta(name="fastq_to_fasta", args={"-i": "qfastq.fq", "-o": "qfasta.fa"})
fq2a.add_dependencies(done=[fqqf])
self.wf = WorkFlow([fqqf, fq2a])
self.fqqf = fqqf
self.fq2a = fq2a
def test_workflow_create_submit_str(self):
"""Display workflow submission commands.
"""
job_list = [
"bsub -J quality_filter -o quality_filter.out fastq_quality_filter -Q 33 -o qfastq.fq -i fastq.fq -p 90 -q 20",
'bsub -J fastq_to_fasta -w "done(quality_filter)" -o fastq_to_fasta.out fastq_to_fasta -o qfasta.fa -i qfastq.fq',
]
for job, jl in zip(self.wf.jobs, job_list):
self.assertEqual(self.wf._create_submit_str(job), jl)
def test_check_jobnames(self):
"""Method makes sure job names are unique.
Raises DuplicateJobNames exception if jobnames are not unique.
"""
qf = FastqQualityFilter(name="job")
qa = FastqToFasta(name="job")
self.assertRaises(DuplicateJobNames, wf=WorkFlow([qf, qa]))
def test_build_bsub(self):
"""_build_bsub is a hidden method building lsf requirement.
"""
bsub_list = [
"bsub -J quality_filter -o quality_filter.out",
'bsub -J fastq_to_fasta -w "done(quality_filter)" -o fastq_to_fasta.out',
]
for job, bl in zip(self.wf.jobs, bsub_list):
self.assertEqual(self.wf._build_bsub(job), bl)
def test_lsf(self):
"""lsf attribute should be true based on setUP.
"""
self.assertTrue(self.wf.lsf)
def test_jobs_attribute(self):
"""setUp initialized two jobs: fqqf + fq2a
"""
self.assertEqual([self.fqqf, self.fq2a], self.wf.jobs)