mkdir inputs &&

        ## Note about compression handling in the following:
        ## guppyplex use mimetypes.guess_type to guess compression so
        ## it's important to get the suffix of the inputs right.
        ## Even if it detects compressed input, it will write uncompressed
        ## output so we need to handle output compression separately.

        ## symlink input files to appropriate names in the inputs/ directory
        bash prepare_inputs.sh &&
        #if str($input.structure) == 'one_to_one':
            #set $compressed = $input.reads.is_of_type("fastq.gz", "fastqsanger.gz")
        #else:
            #set $compressed = next(iter($input.reads)).is_of_type("fastq.gz", "fastqsanger.gz")
        #end if

        artic guppyplex 
            --min-length $min_length 
            --max-length $max_length
        #if $min_quality == 0:
            --skip-quality-check
        #else:
            --quality $min_quality
        #end if
            --directory inputs/
            --output guppyplex_out.fastq
        #if $compressed:
            && gzip guppyplex_out.fastq
        #end if