$ rnftools wgsim2rnf -h

usage: rnftools wgsim2rnf [-h] -1 file [-2 file] -o file -i file [-g int] [-u]

Convert WgSim FASTQ files to RNF-FASTQ.

optional arguments:
  -h, --help            show this help message and exit
  -1 file, --wgsim-fastq-1 file
                        First WgSim FASTQ file (- for standard input)
  -2 file, --wgsim-fastq-2 file
                        Second WgSim FASTQ file (in case of paired-end reads,
                        default: none).
  -o file, --rnf-fastq file
                        Output FASTQ file (- for standard output).
  -i file, --fasta-index file
                        FAI index of the reference FASTA file (- for standard
                        input). It can be created using 'samtools faidx'.
  -g int, --genome-id int
                        Genome ID in RNF (default: 1).
  -u, --allow-unmapped  Allow unmapped reads.
