def tests(self) -> Optional[List[TTestCase]]:
parent_dir = "https://swift.rc.nectar.org.au/v1/AUTH_4df6e734a509497692be237549bbe9af/janis-test-data/bioinformatics"
germline_data = f"{parent_dir}/wgsgermline_data"
somatic_data = f"{parent_dir}/wgssomatic_data"
return [
TTestCase(
name="basic",
input={
"normal_inputs": [[
f"{somatic_data}/NA24385-BRCA1_R1.fastq.gz",
f"{somatic_data}/NA24385-BRCA1_R21.fastq.gz",
]],
"normal_name":
"NA24385-BRCA1",
"tumor_inputs": [[
f"{somatic_data}/NA12878-NA24385-mixture-BRCA1_R1.fastq.gz",
f"{somatic_data}/NA12878-NA24385-mixture-BRCA1_R2.fastq.gz",
]],
"tumor_name":
"NA12878-NA24385-mixture",
"reference":
f"{germline_data}/Homo_sapiens_assembly38.chr17.fasta",
"gridss_blacklist":
f"{somatic_data}/consensusBlacklist.hg38.chr17.bed",
"gnomad":
f"{somatic_data}/af-only-gnomad.hg38.BRCA1.vcf.gz",
"gatk_intervals": [f"{germline_data}/BRCA1.hg38.bed"],
"known_indels":
f"{germline_data}/Homo_sapiens_assembly38.known_indels.BRCA1.vcf.gz",
"mills_indels":
f"{germline_data}/Mills_and_1000G_gold_standard.indels.hg38.BRCA1.vcf.gz",
"snps_1000gp":
f"{germline_data}/1000G_phase1.snps.high_confidence.hg38.BRCA1.vcf.gz",
"snps_dbsnp":
f"{germline_data}/Homo_sapiens_assembly38.dbsnp138.BRCA1.vcf.gz",
"cutadapt_adapters":
f"{germline_data}/contaminant_list.txt",
},
output=BamBai.basic_test("out_normal_bam", 3265300, 49500) +
BamBai.basic_test("out_tumor_bam", 3341700, 49000) +
TextFile.basic_test(
"out_normal_performance_summary",
950,
md5="e3205735e5fe8c900f05050f8ed73f19",
) + TextFile.basic_test(
"out_tumor_performance_summary",
950,
md5="122bfa2ece90c0f030015feba4ba7d84",
) +
FastqGzPair.basic_test("out_normal_fastqc_reports", 881300) +
FastqGzPair.basic_test("out_tumor_fastqc_reports", 874900),
)
]
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={
"bam": [f"{remote_dir}/NA12878-BRCA1.merged.bam"],
"javaOptions": ["-Xmx6G"],
"maxRecordsInRam": 5000000,
"createIndex": True,
"tmpDir": "./tmp",
},
output=BamBai.basic_test(
"out",
2829000,
3780,
f"{remote_dir}/NA12878-BRCA1.markduped.bam.flagstat",
) + TextFile.basic_test(
"metrics",
3700,
"NA12878-BRCA1\t193\t9468\t164\t193\t46\t7\t1\t0.003137\t7465518",
112,
),
)
]
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={
"bam": f"{remote_dir}/NA12878-BRCA1.markduped.bam",
"reference":
f"{remote_dir}/Homo_sapiens_assembly38.chr17.fasta",
"recalFile": f"{remote_dir}/NA12878-BRCA1.markduped.table",
"intervals": f"{remote_dir}/BRCA1.hg38.bed",
},
output=BamBai.basic_test(
"out",
2600000,
21000,
f"{remote_dir}/NA12878-BRCA1.recalibrated.flagstat",
),
),
TTestCase(
name="minimal",
input={
"bam": f"{remote_dir}/NA12878-BRCA1.markduped.bam",
"reference":
f"{remote_dir}/Homo_sapiens_assembly38.chr17.fasta",
"recalFile": f"{remote_dir}/NA12878-BRCA1.markduped.table",
"intervals": f"{remote_dir}/BRCA1.hg38.bed",
},
output=self.minimal_test(),
),
]
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={
"bams": [
f"{remote_dir}/NA12878-BRCA1.sorted.bam",
],
"createIndex": True,
"validationStringency": "SILENT",
"javaOptions": ["-Xmx6G"],
"maxRecordsInRam": 5000000,
"tmpDir": "./tmp",
"useThreading": True,
},
output=BamBai.basic_test(
"out",
2826968,
49688,
f"{remote_dir}/NA12878-BRCA1.bam.flagstat",
"963a51f7feed5b829319b947961b8a3e",
"231c10d0e43766170f5a7cd1b8a6d14e",
),
)
]
def tests(self):
return [
TTestCase(
name="basic",
input={
"bam": [
os.path.join(
BioinformaticsTool.test_data_path(),
"wgsgermline_data",
"NA12878-BRCA1.merged.bam",
)
],
"javaOptions": ["-Xmx6G"],
"maxRecordsInRam": 5000000,
"createIndex": True,
"tmpDir": "./tmp",
},
output=BamBai.basic_test(
"out",
2829000,
3780,
os.path.join(
BioinformaticsTool.test_data_path(),
"wgsgermline_data",
"NA12878-BRCA1.markduped.bam.flagstat",
),
)
+ TextFile.basic_test(
"metrics",
3700,
"NA12878-BRCA1\t193\t9468\t164\t193\t46\t7\t1\t0.003137\t7465518",
112,
),
)
]
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={
"bams": [
f"{remote_dir}/NA12878-BRCA1.sorted.bam",
],
"maxRecordsInRam": 5000000,
"createIndex": True,
"mergeSamFiles_useThreading": True,
"mergeSamFiles_validationStringency": "SILENT",
},
output=BamBai.basic_test(
"out",
2829000,
3780,
f"{remote_dir}/NA12878-BRCA1.markduped.bam.flagstat",
),
),
TTestCase(
name="minimal",
input={
"bams": [
f"{remote_dir}/NA12878-BRCA1.sorted.bam",
],
"maxRecordsInRam": 5000000,
"createIndex": True,
"mergeSamFiles_useThreading": True,
"mergeSamFiles_validationStringency": "SILENT",
},
output=self.minimal_test(),
),
]
def tests(self):
return [
TTestCase(
name="basic",
input={
"bams": [
os.path.join(
BioinformaticsTool.test_data_path(),
"wgsgermline_data",
"NA12878-BRCA1.sorted.bam",
)
],
"createIndex": True,
"validationStringency": "SILENT",
"javaOptions": ["-Xmx6G"],
"maxRecordsInRam": 5000000,
"tmpDir": "./tmp",
"useThreading": True,
},
output=BamBai.basic_test(
"out",
2826968,
49688,
os.path.join(
BioinformaticsTool.test_data_path(),
"wgsgermline_data",
"NA12878-BRCA1.bam.flagstat",
),
"963a51f7feed5b829319b947961b8a3e",
"231c10d0e43766170f5a7cd1b8a6d14e",
),
)
]
def tests(self):
return [
TTestCase(
name="basic",
input={
"bam": os.path.join(
BioinformaticsTool.test_data_path(),
"wgsgermline_data",
"NA12878-BRCA1.recalibrated.bam",
),
"intervals": os.path.join(
BioinformaticsTool.test_data_path(),
"wgsgermline_data",
"BRCA1.hg38.bed",
),
"javaOptions": ["-Xmx3G"],
"outputFilename": ".",
},
output=BamBai.basic_test(
"out",
2600900,
21300,
os.path.join(
BioinformaticsTool.test_data_path(),
"wgsgermline_data",
"NA12878-BRCA1.split.flagstat",
),
),
)
]
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={
"inputRead": f"{remote_dir}/NA12878-BRCA1.split.bam",
"reference": f"{remote_dir}/Homo_sapiens_assembly38.chr17.fasta",
"intervals": f"{remote_dir}/BRCA1.hg38.bed",
"dbsnp": f"{remote_dir}/Homo_sapiens_assembly38.dbsnp138.BRCA1.vcf.gz",
"javaOptions": ["-Xmx6G"],
"pairHmmImplementation": "LOGLESS_CACHING",
},
output=VcfTabix.basic_test(
"out",
12800,
270,
214,
["GATKCommandLine"],
"0224e24e5fc27286ee90c8d3c63373a7",
)
+ BamBai.basic_test(
"bam",
596698,
21272,
f"{remote_dir}/NA12878-BRCA1.haplotyped.flagstat",
"d83b4c0d8eab24a3be1cc6af4f827753",
"b4bb4028b8679a3a635e3ad87126a097",
),
)
]
def tests(self):
return [
TTestCase(
name="basic",
input={
"inputRead":
os.path.join(
BioinformaticsTool.test_data_path(),
"wgsgermline_data",
"NA12878-BRCA1.split.bam",
),
"reference":
os.path.join(
BioinformaticsTool.test_data_path(),
"wgsgermline_data",
"Homo_sapiens_assembly38.chr17.fasta",
),
"intervals":
os.path.join(
BioinformaticsTool.test_data_path(),
"wgsgermline_data",
"BRCA1.hg38.bed",
),
"dbsnp":
os.path.join(
BioinformaticsTool.test_data_path(),
"wgsgermline_data",
"Homo_sapiens_assembly38.dbsnp138.BRCA1.vcf.gz",
),
"javaOptions": ["-Xmx6G"],
"pairHmmImplementation":
"LOGLESS_CACHING",
},
output=VcfTabix.basic_test(
"out",
12800,
270,
214,
["GATKCommandLine"],
"0224e24e5fc27286ee90c8d3c63373a7",
) + BamBai.basic_test(
"bam",
596698,
21272,
os.path.join(
BioinformaticsTool.test_data_path(),
"wgsgermline_data",
"NA12878-BRCA1.haplotyped.flagstat",
),
"d83b4c0d8eab24a3be1cc6af4f827753",
"b4bb4028b8679a3a635e3ad87126a097",
),
)
]
def tests(self):
return [
TTestCase(
name="basic",
input={
"bams": [
os.path.join(
BioinformaticsTool.test_data_path(),
"wgsgermline_data",
"NA12878-BRCA1.sorted.bam",
)
],
"maxRecordsInRam":
5000000,
"createIndex":
True,
"mergeSamFiles_useThreading":
True,
"mergeSamFiles_validationStringency":
"SILENT",
},
output=BamBai.basic_test(
"out",
2829000,
3780,
os.path.join(
BioinformaticsTool.test_data_path(),
"wgsgermline_data",
"NA12878-BRCA1.markduped.bam.flagstat",
),
),
),
TTestCase(
name="minimal",
input={
"bams": [
os.path.join(
BioinformaticsTool.test_data_path(),
"wgsgermline_data",
"NA12878-BRCA1.sorted.bam",
)
],
"maxRecordsInRam":
5000000,
"createIndex":
True,
"mergeSamFiles_useThreading":
True,
"mergeSamFiles_validationStringency":
"SILENT",
},
output=self.minimal_test(),
),
]
def tests(self):
return [
TTestCase(
name="basic",
input={
"bam": os.path.join(
BioinformaticsTool.test_data_path(),
"wgsgermline_data",
"NA12878-BRCA1.markduped.bam",
),
"reference": os.path.join(
BioinformaticsTool.test_data_path(),
"wgsgermline_data",
"Homo_sapiens_assembly38.chr17.fasta",
),
"snps_dbsnp": os.path.join(
BioinformaticsTool.test_data_path(),
"wgsgermline_data",
"Homo_sapiens_assembly38.dbsnp138.BRCA1.vcf.gz",
),
"snps_1000gp": os.path.join(
BioinformaticsTool.test_data_path(),
"wgsgermline_data",
"1000G_phase1.snps.high_confidence.hg38.BRCA1.vcf.gz",
),
"known_indels": os.path.join(
BioinformaticsTool.test_data_path(),
"wgsgermline_data",
"Homo_sapiens_assembly38.known_indels.BRCA1.vcf.gz",
),
"mills_indels": os.path.join(
BioinformaticsTool.test_data_path(),
"wgsgermline_data",
"Mills_and_1000G_gold_standard.indels.hg38.BRCA1.vcf.gz",
),
"intervals": os.path.join(
BioinformaticsTool.test_data_path(),
"wgsgermline_data",
"BRCA1.hg38.bed",
),
},
output=BamBai.basic_test(
"out",
2600000,
21000,
os.path.join(
BioinformaticsTool.test_data_path(),
"wgsgermline_data",
"NA12878-BRCA1.recalibrated.flagstat",
),
),
)
]
def tests(self):
return [
TTestCase(
name="basic",
input={
"bam": os.path.join(
BioinformaticsTool.test_data_path(),
"wgsgermline_data",
"NA12878-BRCA1.bam",
),
"sortOrder": "coordinate",
"createIndex": True,
"maxRecordsInRam": 5000000,
"tmpDir": "./tmp",
"validationStringency": "SILENT",
"javaOptions": ["-Xmx6G"],
},
output=BamBai.basic_test(
"out",
2826980,
49688,
os.path.join(
BioinformaticsTool.test_data_path(),
"wgsgermline_data",
"NA12878-BRCA1.bam.flagstat",
),
"15eb0f8168b42e8ce3ab8b9bc9199e3c",
"a9042025f29f7a08e5f56ce8d11469a1",
),
),
TTestCase(
name="minimal",
input={
"bam": os.path.join(
BioinformaticsTool.test_data_path(),
"wgsgermline_data",
"NA12878-BRCA1.bam",
),
"sortOrder": "coordinate",
"createIndex": True,
"maxRecordsInRam": 5000000,
"tmpDir": "./tmp",
"validationStringency": "SILENT",
"javaOptions": ["-Xmx6G"],
},
output=self.minimal_test(),
),
]
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={
"bam": f"{remote_dir}/NA12878-BRCA1.recalibrated.bam",
"intervals": f"{remote_dir}/BRCA1.hg38.bed",
"javaOptions": ["-Xmx3G"],
"outputFilename": ".",
},
output=BamBai.basic_test(
"out",
2600900,
21300,
f"{remote_dir}/NA12878-BRCA1.split.flagstat",
),
)
]
def tests(self) -> Optional[List[TTestCase]]:
bioinf_base = "https://swift.rc.nectar.org.au/v1/AUTH_4df6e734a509497692be237549bbe9af/janis-test-data/bioinformatics"
hg38 = f"{bioinf_base}/hg38"
chr17 = f"{bioinf_base}/petermac_testdata"
return [
TTestCase(
name="brca1",
input={
"sample_name":
"NA12878",
"reference":
f"{chr17}/Homo_sapiens_assembly38.chr17.fasta",
"fastqs": [[
f"{chr17}/NA12878-BRCA1_R1.fastq.gz",
f"{chr17}/NA12878-BRCA1_R2.fastq.gz",
]],
"gatk_intervals": [f"{chr17}/BRCA1.hg38.bed"],
"known_indels":
f"{chr17}/Homo_sapiens_assembly38.known_indels.BRCA1.vcf.gz",
"mills_indels":
f"{chr17}/Mills_and_1000G_gold_standard.indels.hg38.BRCA1.vcf.gz",
"snps_1000gp":
f"{chr17}/1000G_phase1.snps.high_confidence.hg38.BRCA1.vcf.gz",
"snps_dbsnp":
f"{chr17}/Homo_sapiens_assembly38.dbsnp138.BRCA1.vcf.gz",
"cutadapt_adapters":
f"{chr17}/contaminant_list.txt",
},
output=Vcf.basic_test("out_variants_bamstats", 51300, 230) +
Vcf.basic_test("out_variants_gatk_split", 51300, 221) +
BamBai.basic_test("out_bam", 2822000, 49600) +
TextFile.basic_test(
"out_performance_summary",
948,
md5="575354942cfb8d0367725f9020181443",
) + Array.array_wrapper([
ZipFile.basic_test("out_fastqc_reports", 408000),
ZipFile.basic_test("out_fastqc_reports", 416000),
]),
)
]
def tests(self):
parent_dir = "https://swift.rc.nectar.org.au/v1/AUTH_4df6e734a509497692be237549bbe9af/janis-test-data/bioinformatics"
germline_data = f"{parent_dir}/wgsgermline_data"
somatic_data = f"{parent_dir}/wgssomatic_data"
return [
TTestCase(
name="basic",
input={
"normal_bam": f"{somatic_data}/NA24385-BRCA1.markduped.recalibrated.bam",
"tumor_bam": f"{somatic_data}/NA12878-NA24385-mixture.markduped.recalibrated.bam",
"reference": f"{germline_data}/Homo_sapiens_assembly38.chr17.fasta",
"gnomad": f"{somatic_data}/af-only-gnomad.hg38.BRCA1.vcf.gz",
"intervals": f"{germline_data}/BRCA1.hg38.bed",
"normal_name": "NA24385-BRCA1",
"filterpass_removeFileteredAll": True,
"filterpass_recode": True,
"filterpass_recodeINFOAll": True,
"output_bam_name": "mutect2.bam",
},
output=Vcf.basic_test(
"out",
33000,
147,
["GATKCommandLine"],
"c083775bc8c49397fb65ec12cd435688",
)
+ VcfTabix.basic_test(
"variants",
13000,
260,
182,
["GATKCommandLine"],
"6cfd70dda8599a270978868166ab6545",
)
+ BamBai.basic_test(
"out_bam",
813200,
21200,
f"{somatic_data}/somatic_variant_caller.flagstat",
),
),
]
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={
"bam": f"{remote_dir}/NA12878-BRCA1.markduped.bam",
"reference": f"{remote_dir}/Homo_sapiens_assembly38.chr17.fasta",
"snps_dbsnp": f"{remote_dir}/Homo_sapiens_assembly38.dbsnp138.BRCA1.vcf.gz",
"snps_1000gp": f"{remote_dir}/1000G_phase1.snps.high_confidence.hg38.BRCA1.vcf.gz",
"known_indels": f"{remote_dir}/Homo_sapiens_assembly38.known_indels.BRCA1.vcf.gz",
"mills_indels": f"{remote_dir}/Mills_and_1000G_gold_standard.indels.hg38.BRCA1.vcf.gz",
"intervals": f"{remote_dir}/BRCA1.hg38.bed",
},
output=BamBai.basic_test(
"out",
2600000,
21000,
f"{remote_dir}/NA12878-BRCA1.recalibrated.flagstat",
),
)
]
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={
"bam": f"{remote_dir}/NA12878-BRCA1.bam",
"sortOrder": "coordinate",
"createIndex": True,
"maxRecordsInRam": 5000000,
"tmpDir": "./tmp",
"validationStringency": "SILENT",
"javaOptions": ["-Xmx6G"],
},
output=BamBai.basic_test(
"out",
2826980,
49688,
f"{remote_dir}/NA12878-BRCA1.bam.flagstat",
"15eb0f8168b42e8ce3ab8b9bc9199e3c",
"a9042025f29f7a08e5f56ce8d11469a1",
),
),
TTestCase(
name="minimal",
input={
"bam": f"{remote_dir}/NA12878-BRCA1.bam",
"sortOrder": "coordinate",
"createIndex": True,
"maxRecordsInRam": 5000000,
"tmpDir": "./tmp",
"validationStringency": "SILENT",
"javaOptions": ["-Xmx6G"],
},
output=self.minimal_test(),
),
]
def tests(self):
return [
TTestCase(
name="basic",
input={
"bam": os.path.join(
BioinformaticsTool.test_data_path(),
"wgsgermline_data",
"NA12878-BRCA1.markduped.bam",
),
"reference": os.path.join(
BioinformaticsTool.test_data_path(),
"wgsgermline_data",
"Homo_sapiens_assembly38.chr17.fasta",
),
"recalFile": os.path.join(
BioinformaticsTool.test_data_path(),
"wgsgermline_data",
"NA12878-BRCA1.markduped.table",
),
"intervals": os.path.join(
BioinformaticsTool.test_data_path(),
"wgsgermline_data",
"BRCA1.hg38.bed",
),
},
output=BamBai.basic_test(
"out",
2600000,
21000,
os.path.join(
BioinformaticsTool.test_data_path(),
"wgsgermline_data",
"NA12878-BRCA1.recalibrated.flagstat",
),
),
),
TTestCase(
name="minimal",
input={
"bam": os.path.join(
BioinformaticsTool.test_data_path(),
"wgsgermline_data",
"NA12878-BRCA1.markduped.bam",
),
"reference": os.path.join(
BioinformaticsTool.test_data_path(),
"wgsgermline_data",
"Homo_sapiens_assembly38.chr17.fasta",
),
"recalFile": os.path.join(
BioinformaticsTool.test_data_path(),
"wgsgermline_data",
"NA12878-BRCA1.markduped.table",
),
"intervals": os.path.join(
BioinformaticsTool.test_data_path(),
"wgsgermline_data",
"BRCA1.hg38.bed",
),
},
output=self.minimal_test(),
),
]
def tests(self) -> Optional[List[TTestCase]]:
bioinf_base = "https://swift.rc.nectar.org.au/v1/AUTH_4df6e734a509497692be237549bbe9af/janis-test-data/bioinformatics"
chr17 = f"{bioinf_base}/petermac_testdata"
return [
TTestCase(
name="basic",
input={
"normal_inputs": [[
f"{chr17}/NA24385-BRCA1_R1.fastq.gz",
f"{chr17}/NA24385-BRCA1_R21.fastq.gz",
]],
"normal_name":
"NA24385-BRCA1",
"tumor_inputs": [[
f"{chr17}/NA12878-NA24385-mixture-BRCA1_R1.fastq.gz",
f"{chr17}/NA12878-NA24385-mixture-BRCA1_R2.fastq.gz",
]],
"tumor_name":
"NA12878-NA24385-mixture",
"reference":
f"{chr17}/Homo_sapiens_assembly38.chr17.fasta",
"gridss_blacklist":
f"{chr17}/consensusBlacklist.hg38.chr17.bed",
"gnomad":
f"{chr17}/af-only-gnomad.hg38.BRCA1.vcf.gz",
"gatk_intervals": [f"{chr17}/BRCA1.hg38.bed"],
"known_indels":
f"{chr17}/Homo_sapiens_assembly38.known_indels.BRCA1.vcf.gz",
"mills_indels":
f"{chr17}/Mills_and_1000G_gold_standard.indels.hg38.BRCA1.vcf.gz",
"snps_1000gp":
f"{chr17}/1000G_phase1.snps.high_confidence.hg38.BRCA1.vcf.gz",
"snps_dbsnp":
f"{chr17}/Homo_sapiens_assembly38.dbsnp138.BRCA1.vcf.gz",
"cutadapt_adapters":
f"{chr17}/contaminant_list.txt",
},
output=BamBai.basic_test("out_normal_bam", 3265300, 49500) +
BamBai.basic_test("out_tumor_bam", 3341700, 49000) +
TextFile.basic_test(
"out_normal_performance_summary",
950,
md5="e3205735e5fe8c900f05050f8ed73f19",
) + TextFile.basic_test(
"out_tumor_performance_summary",
950,
md5="122bfa2ece90c0f030015feba4ba7d84",
) + CompressedVcf.basic_test(
"out_variants_gatk",
9040,
147,
["GATKCommandLine"],
"a2e4f96c451754ef8cba80494ed98a70",
) + Vcf.basic_test(
"out_variants",
44090,
156,
["GATKCommandLine"],
"5fc0e861893e0a23f974808265a6917e",
) + Array.array_wrapper([
Vcf.basic_test(
"out_variants_split",
34390,
147,
["GATKCommandLine"],
"c083775bc8c49397fb65ec12cd435688",
)
]) + FastqGzPair.basic_test("out_normal_fastqc_reports",
441500, 439800) +
FastqGzPair.basic_test("out_tumor_fastqc_reports", 434900,
440000),
)
]
