** Describe the bug**
Unicycler crashes when using --spades_options and not using --unicycler_options
To Reproduce
plassembler long -d plassemlber_db -l sample.fastq.gz -o sample_plass -c 600000 --threads 220 --flye_directory metaflye_assemblies/sample_flye --skip_qc --keep_chromosome -f --spades_options "--memory 2000"
Behavior
Internally, this leads Unicycler command to be build like this:
plassembler182/bin/unicycler -s sample_plass/corrected_plasmid_long.fastq -l sample_plass /plasmid_long_entropy_filtered.fastq -t 120 -o sample_plass/unicycler_output None --spades_options '--memory 2000'
Which gives an error of "unicycler: error: unrecognized arguments: None"
** Describe the bug**
Unicycler crashes when using
--spades_optionsand not using--unicycler_optionsTo Reproduce
plassembler long -d plassemlber_db -l sample.fastq.gz -o sample_plass -c 600000 --threads 220 --flye_directory metaflye_assemblies/sample_flye --skip_qc --keep_chromosome -f --spades_options "--memory 2000"Behavior
Internally, this leads Unicycler command to be build like this:
plassembler182/bin/unicycler -s sample_plass/corrected_plasmid_long.fastq -l sample_plass /plasmid_long_entropy_filtered.fastq -t 120 -o sample_plass/unicycler_output None --spades_options '--memory 2000'Which gives an error of "unicycler: error: unrecognized arguments: None"