I'm having problems passing --careful to spades through my nexflow pipline, --spades_options "--phred-offset 33" and --spades_options "--cov-cutoff auto" were no problem but --careful throws the error:
[--spades_options was expecting an argument](unicycler: error: argument --spades_options: expected one argument)
as a note using double quotes, no quotes, and with or without a space at the end didn't seem to help
Passing like this also fails but with a different error
spades.py: error: Please specify option (e.g. -1, -2, -s, etc)) for the following paths: --careful, ''
Using a single dash -careful triggers the same error
It seems unicycler uses --isolate as a deafult which is in compatable with --careful .
There seems to be no way to change this without changing the code myself, future updates maybe?
I'm having problems passing --careful to spades through my nexflow pipline, --spades_options "--phred-offset 33" and --spades_options "--cov-cutoff auto" were no problem but --careful throws the error:
[--spades_options was expecting an argument](unicycler: error: argument --spades_options: expected one argument)
as a note using double quotes, no quotes, and with or without a space at the end didn't seem to help Passing like this also fails but with a different errorspades.py: error: Please specify option (e.g. -1, -2, -s, etc)) for the following paths: --careful, ''
Using a single dash -careful triggers the same error