dnase_template.json

{
    "dnase.replicates": [
        {
            "accession": "",
            "number": ,
            "read_length": 76,
             "adapters": {
                 "sequence_R1": "",
                 "sequence_R2": ""
             },
            "pe_fastqs": [
                {
                    "R1": "",
                    "R2": ""
                }
            ],
            "se_fastqs": null
        }
    ],
    "dnase.references": {
        "genome_name": "GRCh38",
        "indexed_fasta": {
            "fasta": "gs://dnase/ref/GRCh38.fa",
            "fai": "gs://dnase/ref/GRCh38.fa.fai"
        },
        "bwa_index": {
            "bwt": "gs://dnase/ref/GRCh38.fa.bwt",
            "fasta": "gs://dnase/ref/GRCh38.fa",
            "pac": "gs://dnase/ref/GRCh38.fa.pac",
            "ann": "gs://dnase/ref/GRCh38.fa.ann",
            "amb": "gs://dnase/ref/GRCh38.fa.amb",
            "sa": "gs://dnase/ref/GRCh38.fa.sa"
        },
        "nuclear_chroms": "gs://dnase/ref/nuclear_chroms.txt",
        "narrow_peak_auto_sql": "gs://dnase/ref/bigbed/narrowPeak.as",
        "hotspot1": {
            "chrom_info": "gs://dnase/ref/GRCh38.chromInfo.bed",
            "mappable_regions": "gs://dnase/ref/76/GRCh38.K76.mappable_only.bed"
        },
        "hotspot2": {
            "chrom_sizes": "gs://dnase/ref/GRCh38.chrom_sizes.bed",
            "center_sites": "gs://dnase/ref/76/GRCh38.K76.center_sites.n100.starch",
            "mappable_regions": "gs://dnase/ref/76/GRCh38.K76.mappable_only.bed"
        },
        "bias_model": "gs://dnase/ref/vierstra_et_al.txt"
    },
    "dnase.machine_sizes": {
        "align": "large2x",
        "concatenate": "medium",
        "convert": "medium",
        "filter": "large",
        "footprint": "medium2x",
        "mark": "large",
        "merge": "large",
        "normalize": "medium2x",
        "peaks": "medium",
        "qc": "medium",
        "score": "medium",
        "trim": "large2x",
        "unpack": "medium"
    }
}