Allow for no short read input

[LeeBergstrand]

Modify the code so that short reads are no longer required.

Previously, you would have to make mock short read files to get the pipeline to start if you didn't have short reads.

Changes

• Modify CLI
  • modify rotary run_one so the -r1 and -r2 flags are optional.
  • modify rotary init to add a '--no_shortflag to tell therotary` that the input directory contains no short reads.
  • modify rotary and pungi codes so they can read and write a samples.tsv file with only a long sample file column but no short read file columns.
  • modify rotary.smk's set_up_sample_directories rule to take short reads optionally. Also modify it so if there are no short reads that the POLISH_WITH_SHORT_READS parameter is set to False

Limitations

Sample directories can either contain only long and short reads or all long reads, but not a mix of both. The rotary init 's --no_short cannot be activated while importing a directory containing short reads.

[LeeBergstrand]

@jmtsuji This fixes https://github.com/rotary-genomics/rotary/issues/118