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wwood / CoverM

Read coverage calculator for metagenomics
GNU General Public License v3.0
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How can I provide extra parameters to BWA using the "--bwa-params" option? #168

Closed ilnamkang closed 1 year ago

ilnamkang commented 1 year ago

Hi,

I'd like to give extra parameters to BWA, but I can't know how to do it correctly.

Take the "-a" option as an example.

I tried the arguments below, but nothing worked. How can I give extra parameters to BWA?

--bwa-params -a --bwa-params '-a' --bwa-params "-a" --bwa-params a --bwa-params 'a' --bwa-params "a"

Also, error messages likely say that I have to use "--bwa-parameters", not "--bwa-params". What is the correct option to give extra parameters?

Thanks.

wwood commented 1 year ago

Hi,

Sorry I guess the documentation must be incorrect. I'm afk ATM so can't check properly, but maybe try

--bwa-parameters "'-a'"

You could also turn on debug so you know the right call is being made.

ilnamkang commented 1 year ago

Thank you for your quick reply.

I've tested further.

The correct name of the option is "--bwa-parameters", not "--bwa-params".

This option seems to be available in "coverm make", but not in "coverm genome". I was confused because this option is listed on the usage page of "coverm genome". (https://wwood.github.io/CoverM/coverm-genome.html)

For "coverm make", "--bwa-parameters -a" seems to work.

Thanks.

wwood commented 1 year ago

Thanks for this @ilnamkang - it is fixed for the next version i.e. make accepts --bwa-params and --bwa-parameters, either is fine. Closing now.