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={
"reads": [
f"{remote_dir}/NA12878-BRCA1_R1.fastq.gz",
f"{remote_dir}/NA12878-BRCA1_R2.fastq.gz",
],
"threads":
1,
},
output=FastqGzPair.basic_test("out", 824000, 408000, 416000) +
Array.array_wrapper([TextFile.basic_test(
"datafile",
81000,
)]),
),
TTestCase(
name="minimal",
input={
"reads": [
f"{remote_dir}/NA12878-BRCA1_R1.fastq.gz",
f"{remote_dir}/NA12878-BRCA1_R2.fastq.gz",
],
"threads":
1,
},
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"
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) -> 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),
)
]
