{
    "input": "../samplesheet_polyAplus.csv",
    "outdir": "./rnaseq_output",
    "fasta": "../refs/GRCh38.primary_assembly.genome.fa.gz",
    "gtf": "../refs/annotation.gtf.gz",
    "gencode": true,
    "additional_fasta": "../refs/spikeins.fasta.gz",
    "stranded_threshold": 0.7,

    "trimmer": "fastp",
    "extra_fastp_args": "--detect_adapter_for_pe --trim_poly_g --trim_poly_x --dont_eval_duplication",
    "remove_ribo_rna": true,
    "with_umi": false,

    "aligner": "star_rsem",
    "extra_star_align_args": "--alignIntronMax 1000000 --alignIntronMin 20 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMultimapNmax 20 --outFilterType BySJout --outFilterMismatchNoverReadLmax 0.04",

    "skip_alignment": false,
    "skip_pseudo_alignment": true,
    "skip_trimming": false,
    "skip_bigwig": true,
    "skip_bbsplit": true,
    "skip_biotype_qc": false,
    "skip_preseq": false,
    "skip_dupradar": false,
    "skip_stringtie": true,

    "multiqc_title": "ENCODE-whole-cell-nuclear-cytosolic-polyAplus",
    "save_reference": true,
    "publish_dir_mode": "copy",
    "monochrome_logs": true,
}