You must specify an input file of a directory path to a set of input files.
process_radtags 1.35
process_radtags [-f in_file | -p in_dir [-P] [-I] | -1 pair_1 -2 pair_2] -b barcode_file -o out_dir -e enz [-c] [-q] [-r] [-t len] [-D] [-w size] [-s lim] [-h]
  f: path to the input file if processing single-end sequences.
  i: input file type, either 'bustard' for the Illumina BUSTARD format, 'bam', 'fastq' (default), or 'gzfastq' for gzipped FASTQ.
  y: output type, either 'fastq', 'gzfastq', 'fasta', or 'gzfasta' (default is to match the input file type).
  p: path to a directory of files.
  P: files contained within directory specified by '-p' are paired.
  I: specify that the paired-end reads are interleaved in single files.
  1: first input file in a set of paired-end sequences.
  2: second input file in a set of paired-end sequences.
  o: path to output the processed files.
  b: path to a file containing barcodes for this run.
  c: clean data, remove any read with an uncalled base.
  q: discard reads with low quality scores.
  r: rescue barcodes and RAD-Tags.
  t: truncate final read length to this value.
  E: specify how quality scores are encoded, 'phred33' (Illumina 1.8+, Sanger, default) or 'phred64' (Illumina 1.3 - 1.5).
  D: capture discarded reads to a file.
  w: set the size of the sliding window as a fraction of the read length, between 0 and 1 (default 0.15).
  s: set the score limit. If the average score within the sliding window drops below this value, the read is discarded (default 10).
  h: display this help messsage.

  Barcode options:
    --inline_null:   barcode is inline with sequence, occurs only on single-end read (default).
    --index_null:    barcode is provded in FASTQ header (Illumina i5 or i7 read).
    --null_index:    barcode is provded in FASTQ header (Illumina i7 read if both i5 and i7 read are provided).
    --inline_inline: barcode is inline with sequence, occurs on single and paired-end read.
    --index_index:   barcode is provded in FASTQ header (Illumina i5 and i7 reads).
    --inline_index:  barcode is inline with sequence on single-end read and occurs in FASTQ header (from either i5 or i7 read).
    --index_inline:  barcode occurs in FASTQ header (Illumina i5 or i7 read) and is inline with single-end sequence (for single-end data) on paired-end read (for paired-end data).

  Restriction enzyme options:
    -e <enz>, --renz_1 <enz>: provide the restriction enzyme used (cut site occurs on single-end read)
    --renz_2 <enz>: if a double digest was used, provide the second restriction enzyme used (cut site occurs on the paired-end read).
    Currently supported enzymes include:
      'ageI', 'aluI', 'apeKI', 'apoI', 'bamHI', 'bgIII', 'bstYI', 'claI', 
      'ddeI', 'dpnII', 'eaeI', 'ecoRI', 'ecoRV', 'ecoT22I', 'hindIII', 'kpnI', 
      'mluCI', 'mseI', 'mspI', 'ndeI', 'nheI', 'nlaIII', 'notI', 'nsiI', 
      'pstI', 'rsaI', 'sacI', 'sau3AI', 'sbfI', 'sexAI', 'sgrAI', 'speI', 
      'sphI', 'taqI', 'xbaI', or 'xhoI'
  Adapter options:
    --adapter_1 <sequence>: provide adaptor sequence that may occur on the single-end read for filtering.
    --adapter_2 <sequence>: provide adaptor sequence that may occur on the paired-read for filtering.
      --adapter_mm <mismatches>: number of mismatches allowed in the adapter sequence.

  Output options:
    --retain_header: retain unmodified FASTQ headers in the output.
    --merge: if no barcodes are specified, merge all input files into a single output file.

  Advanced options:
    --filter_illumina: discard reads that have been marked by Illumina's chastity/purity filter as failing.
    --disable_rad_check: disable checking if the RAD site is intact.
    --len_limit <limit>: specify a minimum sequence length (useful if your data has already been trimmed).
    --barcode_dist_1: the number of allowed mismatches when rescuing single-end barcodes (default 1).
    --barcode_dist_2: the number of allowed mismatches when rescuing paired-end barcodes (defaults to --barcode_dist_1).