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template.full.json
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template.full.json
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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.ref_fa" : null,
"atac.bowtie2_idx_tar" : null,
"atac.chrsz" : null,
"atac.blacklist" : null,
"atac.gensz" : null,
"atac.tss" : null,
"atac.dnase" : null,
"atac.prom" : null,
"atac.enh" : null,
"atac.reg2map" : null,
"atac.reg2map_bed" : null,
"atac.roadmap_meta" : null,
"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.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.cutadapt_param" : "-e 0.1 -m 5",
"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.bowtie2_param_pe" : "-X2000 --mm --local",
"atac.bowtie2_param_se" : "--local",
"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.keep_irregular_chr_in_bfilt_peak" : false,
"atac.disable_ataqc" : false,
"atac.mito_chr_name" : "chrM",
"atac.regex_filter_reads" : "chrM",
"atac.trim_adapter_cpu" : 2,
"atac.trim_adapter_mem_mb" : 12000,
"atac.trim_adapter_time_hr" : 24,
"atac.trim_adapter_disks" : "local-disk 100 HDD",
"atac.bowtie2_cpu" : 4,
"atac.bowtie2_mem_mb" : 20000,
"atac.bowtie2_time_hr" : 48,
"atac.bowtie2_disks" : "local-disk 200 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.macs2_mem_mb" : 16000,
"atac.macs2_time_hr" : 24,
"atac.macs2_disks" : "local-disk 200 HDD",
"atac.ataqc_mem_mb" : 16000,
"atac.ataqc_mem_java_mb" : 15000,
"atac.ataqc_time_hr" : 24,
"atac.ataqc_disks" : "local-disk 200 HDD"
}