Pipeline crashes when no plasmids found

[dfornika]

In cases where plassembler doesn't find any plasmids, we run into an error because the file unicycler_output/assembly.fasta is not produced:

2024-01-17 10:13:08.929 | WARNING  | plassembler.utils.external_tools:run_tool:113 - Unicycler has failed. This usually means that you have no plasmids. Checking.
  2024-01-17 10:13:08.930 | INFO     | plassembler:run:660 - No plasmids found.
  2024-01-17 10:13:08.930 | INFO     | plassembler:run:661 - Your sample probably has no plasmids.
  2024-01-17 10:13:08.931 | INFO     | plassembler:run:662 - Check the SAMPLE_assembly/plasmid_fastqs/long_plasmid.fastq file.
  2024-01-17 10:13:08.931 | INFO     | plassembler:run:665 - If this is small (indicating few unmapped reads and therefore Unicycler failed due to low depth), then your sample likely has no plasmids.
  2024-01-17 10:13:10.103 | INFO     | plassembler:end_plassembler:117 - Plassembler has finished
  2024-01-17 10:13:10.105 | INFO     | plassembler:end_plassembler:118 - Elapsed time: 2002.0 seconds
  cp: cannot stat 'SAMPLE_assembly/unicycler_output/assembly.fasta': No such file or directory