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…bio-hifi (#83, #84) #83: build the unicycler extra-options suffix via a helper that handles each of unicycler_options / spades_options being None independently. Previously, when only --spades_options was set, a None unicycler_options was interpolated into the command as the literal string "None", so Unicycler failed with "unrecognized arguments: None". #84: map the validated --pacbio_model to canu's read type via a helper. `--pacbio-hifi` now yields `-pacbio-hifi` (the check compared against "pacbio-hifi" without the -- prefix, so HiFi reads were assembled as -pacbio), and canu read correction is skipped for HiFi reads (canu -correct rejects them: "Cannot correct already corrected reads"). Both helpers have unit tests; #83 also validated end-to-end (a real `plassembler long --spades_options` run completes with a clean unicycler command).
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#83: build the unicycler extra-options suffix via a helper that handles each of unicycler_options / spades_options being None independently. Previously, when only --spades_options was set, a None unicycler_options was interpolated into the command as the literal string "None", so Unicycler failed with "unrecognized arguments: None".
#84: map the validated --pacbio_model to canu's read type via a helper.
--pacbio-hifinow yields-pacbio-hifi(the check compared against "pacbio-hifi" without the -- prefix, so HiFi reads were assembled as -pacbio), and canu read correction is skipped for HiFi reads (canu -correct rejects them: "Cannot correct already corrected reads").Both helpers have unit tests; #83 also validated end-to-end (a real
plassembler long --spades_optionsrun completes with a clean unicycler command).