You must specify an input file of a directory path to a set of input files.
process_shortreads 1.35
process_shortreads [-f in_file | -p in_dir [-P] [-I] | -1 pair_1 -2 pair_2] -b barcode_file -o out_dir [-i type] [-y type] [-c] [-q] [-r] [-E encoding] [-t len] [-D] [-w size] [-s lim] [-h]
  f: path to the input file if processing single-end seqeunces.
  i: input file type, either 'bustard' for the Illumina BUSTARD format, 'bam', 'fastq' (default), or 'gzfastq' for gzipped FASTQ.
  p: path to a directory of single-end Illumina files.
  1: first input file in a set of paired-end sequences.
  2: second input file in a set of paired-end sequences.
  P: specify that input is paired (for use with '-p').
  I: specify that the paired-end reads are interleaved in single files.
  o: path to output the processed files.
  y: output type, either 'fastq' or 'fasta' (default fastq).
  b: a list of barcodes for this run.
  c: clean data, remove any read with an uncalled base.
  q: discard reads with low quality scores.
  r: rescue barcodes.
  t: truncate final read length to this value.
  E: specify how quality scores are encoded, 'phred33' (Illumina 1.8+, Sanger) or 'phred64' (Illumina 1.3 - 1.5, default).
  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).

  Adapter options:
    --adapter_1 <sequence>: provide adaptor sequence that may occur on the first 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 (or single pair of files).

  Advanced options:
    --no_read_trimming: do not trim low quality reads, just discard them.
    --len_limit <limit>: when trimming sequences, specify the minimum length a sequence must be to keep it (default 31bp).
    --filter_illumina: discard reads that have been marked by Illumina's chastity/purity filter as failing.
    --barcode_dist: provide the distace between barcodes to allow for barcode rescue (default 2)
    --mate-pair: raw reads are circularized mate-pair data, first read will be reverse complemented.
    --no_overhang: data does not contain an overhang nucleotide between barcode and seqeunce.