{
  "remove_ribo_rna": false,
  "custom_config_base": "https://raw.githubusercontent.com/nf-core/configs/master",
  "skip_deseq2_qc": true,
  "gencode": false,
  "umitools_dedup_stats": false,
  "plaintext_email": false,
  "gene_bed": "",
  "save_reference": false,
  "skip_markduplicates": false,
  "ribo_database_manifest": "/.nextflow/assets/pluto-biosciences/pluto-pipelines-rnaseq/assets/rrna-db-defaults.txt",
  "monochrome_logs": false,
  "aligner": "star_rsem",
  "max_cpus": 32,
  "featurecounts_group_type": "gene_biotype",
  "save_bbsplit_reads": false,
  "skip_multiqc": false,
  "skip_preseq": true,
  "skip_dupradar": false,
  "save_align_intermeds": true,
  "gtf": "<path to organism-specific GTF>",
  "max_multiqc_email_size": "25.MB",
  "use_spot": true,
  "max_time": "240.h",
  "save_trimmed": false,
  "min_trimmed_reads": 10000,
  "pipeline_type": "experiment",
  "skip_fastqc": false,
  "deseq2_vst": true,
  "umitools_extract_method": "string",
  "validate_params": true,
  "config_profile_contact": "Hatem Nawar @hnawar",
  "bam_csi_index": false,
  "with_umi": false,
  "skip_qc": false,
  "version": false,
  "trimmer": "trimgalore",
  "publish_dir_mode": "copy",
  "input": "<path to user-created sample annotation file>",
  "skip_bigwig": false,
  "strandedness": "auto",
  "igenomes_base": "s3://ngi-igenomes/igenomes",
  "stringtie_ignore_gtf": false,
  "config_profile_url": "https://cloud.google.com/batch",
  "use_private_ip": true,
  "skip_umi_extract": false,
  "google_bucket": false,
  "save_unaligned": false,
  "featurecounts_feature_type": "exon",
  "multiqc_title": "<Pluto experiment ID>",
  "custom_config_version": "master",
  "max_memory": "128.GB",
  "boot_disk": "100 GB",
  "fasta": "<path to organism-specific fasta>",
  "hisat2_build_memory": "200.GB",
  "skip_rseqc": false,
  "save_non_ribo_reads": false,
  "skip_alignment": false,
  "skip_qualimap": false,
  "star_index": "",
  "star_ignore_sjdbgtf": false,
  "skip_stringtie": true,
  "gtf_extra_attributes": "gene_name",
  "save_merged_fastq": true,
  "rsem_index": "<path to organism-specific index>",
  "save_umi_intermeds": false,
  "schema_ignore_params": "genomes",
  "config_profile_description": "Google Cloud Batch API Profile",
  "min_mapped_reads": 5,
  "rseqc_modules": "bam_stat,inner_distance,infer_experiment,junction_annotation,junction_saturation,read_distribution,read_duplication",
  "experiment_id": "<Pluto experiment ID>",
  "google_debug": false,
  "gtf_group_features": "gene_id",
  "skip_trimming": false,
  "igenomes_ignore": false,
  "skip_pseudo_alignment": false,
  "outdir": "<path to out directory>",
  "skip_bbsplit": true,
  "genome": "<path to user-selected genome build>",
  "help": false,
  "show_hidden_params": false,
  "test_data_base": "https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3",
  "google_preemptible": true,
  "location": "<GCP region>",
  "umitools_grouping_method": "directional",
  "google_zone": "<GCP zone>",
  "skip_biotype_qc": true
}