nf-params.json

{
    "input": "s3://salzman-lab/nf-sicilian-outputs/aws-maca-full-genome/umitools/extract/*_{1,2}.fastq.gz",
    "single_end": true,
    "outdir": "s3://salzman-lab/nf-sicilian-outputs/aws-maca-full-genome",
    "email": "olga.botvinnik@czbiohub.org",
    "fasta": "http://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M17/GRCm38.p6.genome.fa.gz",
    "gtf": "s3://salzman-lab/sicilian-references/mouse/mm10/gtf_file/GCF_000001635.26_GRCm38.p6_genomic.gtf.gz",
    "star_index": "s3://salzman-lab/nf-sicilian-outputs/aws-maca-full-genome/genome/index/star/",
    "tenx": true,
    "stranded": true,
    "domain": "s3://salzman-lab/hg38_ref_files/domain_file.txt",
    "annotator": "s3://salzman-lab/nf-sicilian-outputs/aws-maca-full-genome/sicilian/GCF_000001635_gene_names.pkl",
    "exon_bounds": "s3://salzman-lab/nf-sicilian-outputs/aws-maca-full-genome/sicilian/GCF_000001635_exon_bounds.pkl",
    "splices": "s3://salzman-lab/nf-sicilian-outputs/aws-maca-full-genome/sicilian/GCF_000001635_splices.pkl",
    "skip_umitools": true
}