{
    "save_spikein_aligned": false,
    "extend_fragments": true,
    "custom_config_base": "https://raw.githubusercontent.com/nf-core/configs/master",
    "dt_heatmap_gene_beforelen": 3000,
    "plaintext_email": false,
    "run_deeptools_qc": false,
    "run_consensus_all": true,
    "run_input_check": true,
    "run_igv": true,
    "aligner": "bowtie2",
    "peakcaller": "<selected peak caller>",
    "only_genome": false,
    "seacr_norm": "non",
    "macs2_pvalue": 0.05,
    "gtf": "<path to file>",
    "save_trimmed": false,
    "clip_r1": 0,
    "clip_r2": 0,
    "skip_fastqc": false,
    "spikein_genome": "Ecoli_K12_MG1655",
    "bowtie2": "<path to file>",
    "minimum_alignment_q_score": 20,
    "run_cat_fastq": true,
    "skip_peak_qc": false,
    "only_preqc": false,
    "trim_nextseq": 0,
    "normalisation_binsize": 50,
    "publish_dir_mode": "copy",
    "input": "<input sample manifest>",
    "only_alignment": false,
    "dt_heatmap_peak_afterlen": 3000,
    "dedup_target_reads": false,
    "enable_conda": false,
    "macs2_broad_cutoff": 0.00001,
    "dt_qc_bam_binsize": 500,
    "config_profile_url": "https://cloud.google.com/batch",
    "use_private_ip": true,
    "run_alignment": true,
    "run_peak_qc": true,
    "three_prime_clip_r1": 0,
    "save_unaligned": false,
    "three_prime_clip_r2": 0,
    "fasta": "<path to user-selected genome>",
    "custom_config_version": "master",
    "run_peak_calling": true,
    "save_align_intermed": true,
    "replicate_threshold": 1,
    "normalisation_c": 10000,
    "macs_gsize": 2940000000,
    "fragment_size": 100,
    "schema_ignore_params": "genomes,callers,dedup_control_only,fragment_size,run_igv,run_multiqc,run_reporting,run_consensus_all,run_peak_calling,run_remove_dups,run_mark_dups,run_read_filter,run_alignment,run_trim_galore_fastqc,run_cat_fastq,run_input_check,run_genome_prep,run_peak_qc,run_deeptools_qc,run_deeptools_heatmaps,run_preseq",
    "only_input": false,
    "min_peak_overlap": 0.2,
    "config_profile_description": "Google Cloud Batch API Profile",
    "run_multiqc": true,
    "google_debug": false,
    "blacklist": "<path to user-selected genome>",
    "skip_trimming": false,
    "seacr_peak_threshold": 0.05,
    "skip_removeduplicates": false,
    "use_control": true,
    "outdir": "<oudir>",
    "genome": "<path to user-selected genome>",
    "help": false,
    "normalisation_mode": "CPM",
    "run_reporting": true,
    "run_coverage": true,
    "save_reference": true,
    "monochrome_logs": false,
    "max_cpus": 32,
    "igv_show_gene_names": true,
    "skip_multiqc": false,
    "skip_preseq": false,
    "igg_scale_factor": 0.5,
    "max_multiqc_email_size": "25.MB",
    "use_spot": true,
    "max_time": "240.h",
    "skip_heatmaps": true,
    "pipeline_type": "experiment",
    "tracedir": "<outdir for pipeline info>",
    "validate_params": true,
    "config_profile_contact": "Hatem Nawar @hnawar",
    "consensus_peak_mode": "all",
    "run_trim_galore_fastqc": true,
    "only_filtering": false,
    "igenomes_base": "s3://ngi-igenomes/igenomes/",
    "spikein_fasta": "<path to genome.fa>",
    "dt_heatmap_gene_bodylen": 5000,
    "skip_igv": false,
    "run_remove_dups": true,
    "google_bucket": false,
    "multiqc_title": "<experiment ID>",
    "max_memory": "128.GB",
    "boot_disk": "100 GB",
    "run_preseq": true,
    "dt_heatmap_gene_afterlen": 3000,
    "run_mark_dups": true,
    "save_merged_fastq": true,
    "skip_dt_qc": false,
    "run_genome_prep": true,
    "experiment_id": "<experiment ID>",
    "only_peak_calling": false,
    "skip_reporting": false,
    "igenomes_ignore": false,
    "run_deeptools_heatmaps": false,
    "spikein_bowtie2": "<path to Bowtie2Index>",
    "macs2_narrow_peak": false,
    "min_frip_overlap": 0.2,
    "dt_heatmap_peak_beforelen": 3000,
    "run_read_filter": true,
    "show_hidden_params": false,
    "google_preemptible": true,
    "location": "us-central1",
    "callers": [
        "<selected peak caller>"
    ],
    "google_zone": "<workspace region>"
}