def test_check_illumina_qc_outputs_singlecell_some_missing(self):
"""
check_illumina_qc_outputs: some illumina_qc.sh outputs 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)
# Add QC artefacts
project = AnalysisProject("PJB", os.path.join(self.wd, "PJB"))
UpdateAnalysisProject(project).add_qc_outputs(
include_fastq_strand=False, include_multiqc=False)
# Remove some outputs
for f in (
"PJB1_S1_R2_001_fastqc.html",
"PJB1_S1_R2_001_model_organisms_screen.txt",
):
os.remove(os.path.join(project.qc_dir, f))
# Check
self.assertEqual(
check_illumina_qc_outputs(project,
qc_dir="qc",
qc_protocol="singlecell"),
[os.path.join(project.fastq_dir, "PJB1_S1_R2_001.fastq.gz")])
def test_check_illumina_qc_outputs_standardSE_all_missing(self):
"""
check_illumina_qc_outputs: all illumina_qc.sh outputs missing (standardSE)
"""
# Make mock analysis project
p = MockAnalysisProject("PJB", ("PJB1_S1_R1_001.fastq.gz", ),
metadata={'Organism': 'Human'})
p.create(top_dir=self.wd)
# Get the outputs
project = AnalysisProject("PJB", os.path.join(self.wd, "PJB"))
# Check
self.assertEqual(
check_illumina_qc_outputs(project,
qc_dir="qc",
qc_protocol="standardSE"),
project.fastqs)
def test_check_illumina_qc_outputs_standardSE_all_present(self):
"""
check_illumina_qc_outputs: all illumina_qc.sh outputs present (standardSE)
"""
# Make mock analysis project
p = MockAnalysisProject("PJB", ("PJB1_S1_R1_001.fastq.gz", ),
metadata={'Organism': 'Human'})
p.create(top_dir=self.wd)
# Add QC artefacts
project = AnalysisProject("PJB", os.path.join(self.wd, "PJB"))
UpdateAnalysisProject(project).add_qc_outputs(
include_fastq_strand=False, include_multiqc=False)
# Check
self.assertEqual(
check_illumina_qc_outputs(project,
qc_dir="qc",
qc_protocol="standardSE"), [])