{
    "skip_fastp": true,
    "trim_fastq": false,
    "clip_r1": 28,
    "three_prime_clip_r1": 5,
    "three_prime_adapter": "AAAAAAAGTCGGAGGCCAAGCGGTCT",
    "mirtrace_species": "dre",
    "mirgenedb_species": "Dre",
    "fasta": "~/dir_db/reference_genomes/GRCz11_BOWTIE/NCBI/GCF_000002035.6_GRCz11_genomic.fna",
    "mirna_gtf": "~/dir_db/miRBase/dre.gff3",
    "mature": "~/dir_db/miRBase/mature.fa",
    "hairpin": "~/dir_db/miRBase/hairpin.fa",
    "mirgenedb": true,
    "mirgenedb_gff": "~/dir_db/MirGeneDB_3.0/ALL.gff",
    "mirgenedb_mature": "~/dir_db/MirGeneDB_3.0/ALL-mature.fas",
    "mirgenedb_hairpin": "~/dir_db/MirGeneDB_3.0/ALL-pre.fas",
    "bowtie_index": "~/dir_db/reference_genomes/GRCz11_BOWTIE/NCBI",
    "save_reference": true,
    "filter_contamination": true,
    "rrna": "",
    "trna": "",
    "cdna": "~/dir_db/RNA_contamination_filtering/cDNA/Homo_sapiens.GRCh38.cdna.all.fa.gz",
    "ncrna": "~/dir_db/RNA_contamination_filtering/ncRNA/Homo_sapiens.GRCh38.ncrna.fa.gz",
    "pirna": "",
    "other_contamination": ""
    
}