ENCSR356KRQ_subsampled.json

gistfile1.txt

```
    "atac.pipeline_type" : "atac",
    "atac.genome_tsv" : "/project2/name1/name2/DLDS/process_data/hg19db/hg19.tsv",
    "atac.fastqs" : [
        [
            ["/project2/name1/name2/DLDS/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF341MYG.subsampled.400.fastq.gz",
             "/project2/name1/name2/DLDS/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF248EJF.subsampled.400.fastq.gz"],
            ["/project2/name1/name2/DLDS/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF106QGY.subsampled.400.fastq.gz",
             "/project2/name1/name2/DLDS/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF368TYI.subsampled.400.fastq.gz"]
        ],
        [
            ["/project2/name1/name2/DLDS/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF641SFZ.subsampled.400.fastq.gz",
             "/project2/name1/name2/DLDS/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF031ARQ.subsampled.400.fastq.gz"],
            ["/project2/name1/name2/DLDS/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF751XTV.subsampled.400.fastq.gz",
             "/project2/name1/name2/DLDS/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF590SYZ.subsampled.400.fastq.gz"],
            ["/project2/name1/name2/DLDS/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF927LSG.subsampled.400.fastq.gz",
             "/project2/name1/name2/DLDS/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF734PEQ.subsampled.400.fastq.gz"],
            ["/project2/name1/name2/DLDS/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF859BDM.subsampled.400.fastq.gz",
             "/project2/name1/name2/DLDS/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF007USV.subsampled.400.fastq.gz"],
            ["/project2/name1/name2/DLDS/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF193RRC.subsampled.400.fastq.gz",
             "/project2/name1/name2/DLDS/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF886FSC.subsampled.400.fastq.gz"],
            ["/project2/name1/name2/DLDS/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF366DFI.subsampled.400.fastq.gz",
             "/project2/name1/name2/DLDS/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF573UXK.subsampled.400.fastq.gz"]
        ]
    ],

    "atac.paired_end" : true,
    "atac.multimapping" : 4,

    "atac.trim_adapter.auto_detect_adapter" : true,
    "atac.trim_adapter.cpu" : 1,

    "atac.bowtie2.cpu" : 2,
    "atac.bowtie2.mem_mb" : 16000,

    "atac.filter.cpu" : 1,
    "atac.filter.mem_mb" : 12000,

    "atac.macs2_mem_mb" : 16000,

    "atac.smooth_win" : 73,
    "atac.enable_idr" : true,
    "atac.idr_thresh" : 0.05,

    "atac.qc_report.name" : "ENCSR356KRQ (subsampled 1/400 reads)",
    "atac.qc_report.desc" : "ATAC-seq on primary keratinocytes in day 0.0 of differentiation"
}

```