config.template.yaml

# specify path of input files
# RELATIVE PATH here will use working directory as their origin
genome:
    fasta: test_data/genome/genome.fa
    gtf: test_data/gtf/original.gtf
    # specify existing index file if they are alread built
    # lr2rmats will build them if they do not exist
    minimap_idx_file: test_data/genome/genome.fa.smmi
    star_idx_dir: test_data/genome/genome.STAR

sample:
    long_read:
        samp1: test_data/read/samp1_long.fa
        #samp2: test_data/read/samp2_long.fa
    short_read: # if short-read is single-end, just leave `second` empty, like `second: [] `
        samp1: 
            first: test_data/read/samp1_short_1.fa 
            second: test_data/read/samp1_short_2.fa
        #samp2: 
            #first: test_data/read/samp2_short_single.fa 
            #second: []

# specify path of output file
# RELATIVE PATH here will use working directory as their origin
output:
    updated_gtf: output/updated.gtf # file name of updated GTF
    
# add all execuatable files to PATH, or put their ABSOLUTE paths here
exe_files:
    samtools: samtools
    bedtools: bedtools
    minimap2: minimap2
    star: STAR
    lr2rmats: lr2rmats
    sort_gtf: sort_gtf.sh

# allocate computing resource
__default__:
    h_data: 4G
    h_rt: 02:00:00
    threads: 8

star_idx:
    h_data: 4G
    h_rt: 02:00:00
    threads: 8

star_map:
    h_data: 4G
    h_rt: 02:00:00
    threads: 8

novel_gtf:
    h_data: 4G
    h_rt: 02:00:00
    threads: 1

minimap_idx:
    h_data: 4G
    h_rt: 02:00:00
    threads: 8

minimap_map:
    h_data: 4G
    h_rt: 02:00:00
    threads: 8

lr2rmats:
    rm_gtf: test_data/gtf/rRNA.gtf
    aln_cov: 0.67
    iden_frac: 0.75
    sec_rat: 0.98
    sup_cnt: 1
    split_trans: -s
    full_level: 3