$ rnftools curesim2rnf -h

usage: rnftools curesim2rnf [-h] -c file -o file -i file [-g int]

Convert a CuReSim FASTQ file to RNF-FASTQ.

optional arguments:
  -h, --help            show this help message and exit
  -c file, --curesim-fastq file
                        CuReSim FASTQ file (- for standard input).
  -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).
