template.json

{
    "atac.title" : "Example (paired end)",
    "atac.description" : "This is a template input JSON for paired ended sample.",

    "atac.pipeline_type" : "atac",
    "atac.align_only" : false,
    "atac.true_rep_only" : false,

    "atac.genome_tsv" : "/path_to_genome_data/hg38/hg38.tsv",

    "atac.paired_end" : true,

    "atac.fastqs_rep1_R1" : [ "rep1_R1_L1.fastq.gz", "rep1_R1_L2.fastq.gz", "rep1_R1_L3.fastq.gz" ],
    "atac.fastqs_rep1_R2" : [ "rep1_R2_L1.fastq.gz", "rep1_R2_L2.fastq.gz", "rep1_R2_L3.fastq.gz" ],
    "atac.fastqs_rep2_R1" : [ "rep2_R1_L1.fastq.gz", "rep2_R1_L2.fastq.gz" ],
    "atac.fastqs_rep2_R2" : [ "rep2_R2_L1.fastq.gz", "rep2_R2_L2.fastq.gz" ],

    "atac.adapter" : "AATTCCGG",
    "atac.adapters_rep1_R1" : [ "AATTCCGG", "AATTCCGG", "AATTCCGG" ],
    "atac.adapters_rep1_R2" : [ "AATTCCGG", "AATTCCGG" ],
    "atac.adapters_rep2_R1" : [ "AATTCCGG", "AATTCCGG", "AATTCCGG" ],
    "atac.adapters_rep2_R2" : [ "AATTCCGG", "AATTCCGG" ],
    "atac.auto_detect_adapter" : false,

    "atac.bams" : [
        "raw_rep1.bam",
        "raw_rep2.bam"
    ],

    "atac.nodup_bams" : [
        "nodup_rep1.bam",
        "nodup_rep2.bam"
    ],

    "atac.tas" : [
        "rep1.tagAlign.gz",
        "rep2.tagAlign.gz"
    ],

    "atac.multimapping" : 4,
    "atac.enable_xcor" : false,
    "atac.enable_idr" : true,
    "atac.idr_thresh" : 0.05,
    "atac.disable_ataqc" : false
}