plassembler long passes wrong commands to canu for pacbio-hifi

[Kincekara]

Describe the bug
When plassembler long is run with --pacbio_model pacbio-hifi flag, the program runs canu with -pacbio flag instead of -pacbio-hifi

pacbio_model is set to --pacbio-hifi in here (possibly for the flye):

plassembler/src/plassembler/utils/input_commands.py

Lines 391 to 396 in 8f78420

	elif pacbio_model == "pacbio-hifi":
	message = (
	"You have selected pacbio-hifi designed for PacBio HiFi reads (<1% error)."
	)
	logger.info(message)
	pacbio_model = "--pacbio-hifi"

So it falls into the else condition here:

plassembler/src/plassembler/__init__.py

Lines 1580 to 1588 in 8f78420

	if pacbio_model != "nothing":
	if pacbio_model == "pacbio-hifi":
	canu_nano_or_pacbio = "pacbio-hifi"
	corrected_error_rate = 0.005
	else:
	canu_nano_or_pacbio = "pacbio"
	corrected_error_rate = 0.045
	else:
	canu_nano_or_pacbio = "nanopore"

Although a simple change of if condition to if pacbio_model == "--pacbio-hifi": fixes the logic, it creates another problem below, because hifi reads are considered as corrected.

-- ERROR:
-- ERROR:  Cannot correct already corrected or already trimmed reads.
-- ERROR:   - If the reads are raw (uncorrected), or to run
-- ERROR:     correction again, remove '-corrected'.
-- ERROR:   - Otherwise, remove the '-correct' option.
-- ERROR:

To Reproduce
I used PacBio's public data here:
https://downloads.pacbcloud.com/public/dataset/2021-11-Microbial-96plex/demultiplexed-reads/m64004_210929_143746.bc2001.bam

[Kincekara]

I believe the canu correction can be removed completely for hifi reads.

[gbouras13]

Hi @Kincekara - thanks for reporting, this will be fixed in v1.8.3