atac-seq-pipeline/example_input_json/template.full.json at master · CollinsLabBioComp/atac-seq-pipeline · GitHub

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{
    "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.paired_ends" : [true, 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.read_len" : [],

    "atac.auto_detect_adapter" : false,
    "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.cutadapt_param" : "-e 0.1 -m 5",

    "atac.multimapping" : 4,

    "atac.mapq_thresh" : 30,
    "atac.dup_marker" : "picard",
    "atac.no_dup_removal" : false,

    "atac.subsample_reads" : 0,
    "atac.xcor_subsample_reads" : 25000000,

    "atac.cap_num_peak" : 300000,
    "atac.pval_thresh" : 0.01,
    "atac.smooth_win" : 73,

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

    "atac.enable_xcor" : false,
    "atac.enable_count_signal_track" : false,

    "atac.filter_chrs" : ["chrM", "MT"],

    "atac.enable_preseq" : false,
    "atac.enable_compare_to_roadmap" : false,
    "atac.enable_tss_enrich" : true,
    "atac.enable_gc_bias" : true,

    "atac.align_cpu" : 4,
    "atac.align_mem_mb" : 20000,
    "atac.align_time_hr" : 48,
    "atac.align_disks" : "local-disk 400 HDD",

    "atac.filter_cpu" : 2,
    "atac.filter_mem_mb" : 20000,
    "atac.filter_time_hr" : 24,
    "atac.filter_disks" : "local-disk 400 HDD",

    "atac.bam2ta_cpu" : 2,
    "atac.bam2ta_mem_mb" : 10000,
    "atac.bam2ta_time_hr" : 6,
    "atac.bam2ta_disks" : "local-disk 100 HDD",

    "atac.spr_mem_mb" : 16000,

    "atac.xcor_cpu" : 2,
    "atac.xcor_mem_mb" : 16000,
    "atac.xcor_time_hr" : 6,
    "atac.xcor_disks" : "local-disk 100 HDD",

    "atac.call_peak_mem_mb" : 16000,
    "atac.call_peak_time_hr" : 24,
    "atac.call_peak_disks" : "local-disk 200 HDD",

    "atac.macs2_signal_track_mem_mb" : 16000,
    "atac.macs2_signal_track_time_hr" : 24,
    "atac.macs2_signal_track_disks" : "local-disk 400 HDD",

    "atac.preseq_mem_mb" : 16000,

    "atac.filter_picard_java_heap" : "4G",
    "atac.preseq_picard_java_heap" : "6G",
    "atac.fraglen_stat_picard_java_heap" : "6G",
    "atac.gc_bias_picard_java_heap" : "6G"
}