--sample_sheet                path of the sample sheet
--library                     random_intron, random_exon, muta_intron, muta_exon, default: random_intron
--outdir                      the directory path of output results, default: the current directory

Basic:
--do_pe_reads                 whether to process paired-end reads, default: false
--canonical_method            the method of detecting canonical splicing events, align or match, default: match

Fastp:
--fastp_cut_mean_quality      mean quality for fastp, default: 20

Flash2:
--flash2_min_overlap          min overlap for flash2, default: 10
--flash2_max_overlap          max overlap for flash2, default: 250
--flash2_min_overlap_outie    min overlap outie for flash2, default: 20
--flash2_max_mismatch_density max mismatch density for flash2, default: 0.25

BWA:
--bwa_mismatch                mismatch penalty for BWA, default: 4
--bwa_gap_open                gap open penalty for BWA, default: 10,10
--bwa_gap_ext                 gap extension penalty for BWA, default: 5,5
--bwa_clip                    clip penalty for BWA, default: 1,1
--filter_softclip_base        softclip base for filtering, default: 5

HISAT2:
--hisat2_score_min            min score for HISAT2, default: L,0,-0.3
--hisat2_mp                   min/max mismatch penalty for HISAT2, default: 5,2
--hisat2_sp                   min/max splice penalty for HISAT2, default: 2,1
--hisat2_np                   non-canonical splicing penalty for HISAT2, default: 0
--hisat2_pen_noncansplice     non-canonical splicing penalty for HISAT2, default: 0

Spliced products:
--do_spliced_products         whether to process spliced products, default: false

Regtools:
--regtools_min_anchor         min anchor length for regtools, default: 5
--regtools_min_intron         min intron length for regtools, default: 20

Junction classification:
--classify_min_overlap        min overlap for classification, default: 2
--classify_min_cov            min coverage for classification, default: 2
--classify_reduce             reduce the number of reads for classification, default: 2