chip-seq-pipeline2/example_input_json/template.full.json at master · CollinsLabBioComp/chip-seq-pipeline2 · GitHub

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{
    "chip.title" : "Example (paired-end)",
    "chip.description" : "This is an template input JSON for paired-end sample.",

    "chip.pipeline_type" : "tf",
    "chip.aligner" : "bowtie2",
    "chip.align_only" : false,
    "chip.true_rep_only" : false,

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

    "chip.paired_end" : true,
    "chip.ctl_paired_end" : true,

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

    "chip.ctl_fastqs_rep1_R1" : [ "ctl1_R1.fastq.gz" ],
    "chip.ctl_fastqs_rep1_R2" : [ "ctl1_R2.fastq.gz" ],
    "chip.ctl_fastqs_rep2_R1" : [ "ctl2_R1.fastq.gz" ],
    "chip.ctl_fastqs_rep2_R2" : [ "ctl2_R2.fastq.gz" ],

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

    "chip.subsample_reads" : 0,
    "chip.ctl_subsample_reads" : 0,
    "chip.xcor_subsample_reads" : 15000000,

    "chip.xcor_pe_trim_bp" : 50,
    "chip.use_filt_pe_ta_for_xcor" : false,

    "chip.always_use_pooled_ctl" : false,
    "chip.ctl_depth_ratio" : 1.2,

    "chip.peak_caller" : null,
    "chip.cap_num_peak_macs2" : 500000,
    "chip.pval_thresh" : 0.01,
    "chip.idr_thresh" : 0.05,
    "chip.cap_num_peak_spp" : 300000,

    "chip.enable_jsd" : true,
    "chip.enable_gc_bias" : true,
    "chip.enable_count_signal_track" : false,

    "chip.filter_chrs" : [],

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

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

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

    "chip.spr_mem_mb" : 16000,

    "chip.jsd_cpu" : 2,
    "chip.jsd_mem_mb" : 12000,
    "chip.jsd_time_hr" : 6,
    "chip.jsd_disks" : "local-disk 200 HDD",

    "chip.xcor_cpu" : 2,
    "chip.xcor_mem_mb" : 16000,
    "chip.xcor_time_hr" : 24,
    "chip.xcor_disks" : "local-disk 100 HDD",

    "chip.call_peak_cpu" : 2,
    "chip.call_peak_mem_mb" : 16000,
    "chip.call_peak_time_hr" : 72,
    "chip.call_peak_disks" : "local-disk 200 HDD",

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

    "chip.filter_picard_java_heap" : "4G",
    "chip.gc_bias_picard_java_heap" : "6G"
}