[Feature Request] - Optionally output unaligned reads as fastq

[jolespin]

I'd like to swap out Bowtie2 with Strobealign for my VEBA software suite (https://github.com/jolespin/veba) and several other workflows that I use for preprocessing.

Here's the Bowtie2 command I typically run:

    os.environ["bowtie2"],
    "-x {}".format(opts.contamination_index),
    "-p {}".format(opts.n_jobs),
    "-1 {}".format(input_filepaths[0]),
    "-2 {}".format(input_filepaths[1]),
    "--seed {}".format(opts.random_state),
    "--un-conc {}".format(os.path.join(output_directory, "TMP__cleaned_%.fastq")), #write pairs that didn't align concordantly to <path>
    "--al-conc {}".format(os.path.join(output_directory, "TMP__contaminated_%.fastq")),#write pairs that aligned concordantly at least once to <path>
    opts.bowtie2_options,

Would it be possible to add support for outputting unaligned reads?