def METHOD_NAME(self):
    base = Path("wgs")
    inputs = base / "input"
    outputs = base / "output"
    with self.preparation_stage():
        ref_seq = self.run_process(
            "upload-fasta-nucl",
            {
                "src": inputs / "hs_b37_chr17_upto_TP53.fasta.gz",
                "species": "Homo sapiens",
                "build": "custom_build",
            },
        )
        bwa_index = self.run_process("bwamem2-index", {"ref_seq": ref_seq.id})
        reads = self.prepare_paired_reads(
            mate1=[inputs / "TP53_1.fastq.gz"],
            mate2=[inputs / "TP53_2.fastq.gz"],
        )
        dbsnp = self.run_process(
            "upload-variants-vcf",
            {
                "src": inputs / "dbsnp_TP53.vcf.gz",
                "species": "Homo sapiens",
                "build": "custom_build",
            },
        )
        intervals = self.run_process(
            "upload-bed",
            {
                "src": inputs / "hg38.intervals.bed",
                "species": "Homo sapiens",
                "build": "hg19",
            },
        )
        adapters = self.prepare_ref_seq()
    self.run_process(
        "workflow-wgs-gvcf",
        {
            "reads": reads.id,
            "ref_seq": ref_seq.id,
            "bwa_index": bwa_index.id,
            "known_sites": [dbsnp.id],
            "gatk_options": {
                "intervals": intervals.id,
            },
            "trimming_options": {
                "enable_trimming": True,
                "adapters": adapters.id,
                "seed_mismatches": 2,
                "simple_clip_threshold": 10,
                "min_adapter_length": 8,
                "palindrome_clip_threshold": 30,
                "leading": 20,
                "trailing": 3,
                "minlen": 40,
            },
        },
    )
    for data in Data.objects.all():
        self.assertStatus(data, Data.STATUS_DONE)
    variants = Data.objects.filter(process__slug="gatk-haplotypecaller-gvcf").last()
    self.assertFile(
        variants,
        "vcf",
        outputs / "variants_from_workflow.g.vcf.gz",
        file_filter=filter_vcf_variable,
        compression="gzip",
    )