def tests(self):
remote_dir = "https://swift.rc.nectar.org.au/v1/AUTH_4df6e734a509497692be237549bbe9af/janis-test-data/bioinformatics/wgsgermline_data"
return [
TTestCase(
name="basic",
input={
"sam": f"{remote_dir}/NA12878-BRCA1.bwamem.stdout",
"reference":
f"{remote_dir}/Homo_sapiens_assembly38.chr17.fasta",
"threads": 16,
},
output=Bam.basic_test(
"out",
2740774,
f"{remote_dir}/NA12878-BRCA1.bam.flagstat",
"9a6af420f287df52a122ac723f41b535",
),
),
TTestCase(
name="minimal",
input={
"sam": f"{remote_dir}/NA12878-BRCA1.bwamem.stdout",
"reference":
f"{remote_dir}/Homo_sapiens_assembly38.chr17.fasta",
"threads": 16,
},
output=self.minimal_test(),
),
]
def tests(self):
return [
TTestCase(
name="basic",
input={
"sam":
os.path.join(
BioinformaticsTool.test_data_path(),
"wgsgermline_data",
"NA12878-BRCA1.bwamem.stdout",
),
"reference":
os.path.join(
BioinformaticsTool.test_data_path(),
"wgsgermline_data",
"Homo_sapiens_assembly38.chr17.fasta",
),
"threads":
16,
},
output=Bam.basic_test(
"out",
2740774,
os.path.join(
BioinformaticsTool.test_data_path(),
"wgsgermline_data",
"NA12878-BRCA1.bam.flagstat",
),
"9a6af420f287df52a122ac723f41b535",
),
),
TTestCase(
name="minimal",
input={
"sam":
os.path.join(
BioinformaticsTool.test_data_path(),
"wgsgermline_data",
"NA12878-BRCA1.bwamem.stdout",
),
"reference":
os.path.join(
BioinformaticsTool.test_data_path(),
"wgsgermline_data",
"Homo_sapiens_assembly38.chr17.fasta",
),
"threads":
16,
},
output=self.minimal_test(),
),
]
def tests(self):
return [
TTestCase(
name="basic",
input={
"reads": [
os.path.join(
BioinformaticsTool.test_data_path(),
"wgsgermline_data",
"NA12878-BRCA1_R1.fastq.gz",
),
os.path.join(
BioinformaticsTool.test_data_path(),
"wgsgermline_data",
"NA12878-BRCA1_R2.fastq.gz",
),
],
"reference":
os.path.join(
BioinformaticsTool.test_data_path(),
"wgsgermline_data",
"Homo_sapiens_assembly38.chr17.fasta",
),
"markShorterSplits":
True,
"readGroupHeaderLine":
"@RG\tID:NA12878-BRCA1\tSM:NA12878-BRCA1\tLB:NA12878-BRCA1\tPL:ILLUMINA",
"threads":
16,
},
output=Bam.basic_test(
"out",
8628527,
os.path.join(
BioinformaticsTool.test_data_path(),
"wgsgermline_data",
"NA12878-BRCA1.bwamem.flagstat",
),
),
),
TTestCase(
name="minimal",
input={
"reads": [
os.path.join(
BioinformaticsTool.test_data_path(),
"wgsgermline_data",
"NA12878-BRCA1_R1.fastq.gz",
),
os.path.join(
BioinformaticsTool.test_data_path(),
"wgsgermline_data",
"NA12878-BRCA1_R2.fastq.gz",
),
],
"reference":
os.path.join(
BioinformaticsTool.test_data_path(),
"wgsgermline_data",
"Homo_sapiens_assembly38.chr17.fasta",
),
"markShorterSplits":
True,
"readGroupHeaderLine":
"@RG\tID:NA12878-BRCA1\tSM:NA12878-BRCA1\tLB:NA12878-BRCA1\tPL:ILLUMINA",
"threads":
16,
},
output=self.minimal_test(),
),
]