template.json

{
    "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.always_use_pooled_ctl" : 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" ]
}