def test_check_fastq_strand_outputs_singlecell_missing(self):
"""
check_fastq_strand_outputs: fastq_strand.py output missing (singlecell)
"""
# Make mock analysis project
p = MockAnalysisProject("PJB", (
"PJB1_S1_R1_001.fastq.gz",
"PJB1_S1_R2_001.fastq.gz",
),
metadata={'Organism': 'Human'})
p.create(top_dir=self.wd)
project = AnalysisProject("PJB", os.path.join(self.wd, "PJB"))
# Make fastq_strand.conf
fastq_strand_conf = os.path.join(project.dirn, "fastq_strand.conf")
with open(fastq_strand_conf, 'w') as fp:
fp.write("")
# Check the outputs
self.assertEqual(
check_fastq_strand_outputs(project,
"qc",
fastq_strand_conf,
qc_protocol="singlecell"),
[
(os.path.join(project.fastq_dir, "PJB1_S1_R2_001.fastq.gz"), ),
])
def test_check_fastq_strand_outputs_standardSE_present(self):
"""
check_fastq_strand_outputs: fastq_strand.py output present (standardSE)
"""
# Make mock analysis project
p = MockAnalysisProject("PJB", ("PJB1_S1_R1_001.fastq.gz", ),
metadata={'Organism': 'Human'})
p.create(top_dir=self.wd)
project = AnalysisProject("PJB", os.path.join(self.wd, "PJB"))
UpdateAnalysisProject(project).add_qc_outputs(
protocol="standardSE",
include_fastq_strand=True,
include_multiqc=False)
fastq_strand_conf = os.path.join(project.dirn, "fastq_strand.conf")
# Check the outputs
self.assertEqual(
check_fastq_strand_outputs(project,
"qc",
fastq_strand_conf,
qc_protocol="standardSE"), [])