Syntax confusion regarding sequencing_platform

[JohnUrban]

Hi,

Thanks for the cool tool. I hope to get it running.

I have been trying to get it run with the following command syntax:

${GALA} ${DRAFTS} -a canu fq ${READS} -nanopore-corrected

It gave this error:

usage: gala -h  [options] <draft_names & paths> <fa/fq> <reads> <platform>
gala: error: the following arguments are required: draft_names, input_file, reads, sequencing_platform

I tried taking out -a canu, it gave a new error:

${GALA} ${DRAFTS} -fq ${READS} -nanopore-corrected


usage: gala -h  [options] <draft_names & paths> <fa/fq> <reads> <platform>
gala: error: the following arguments are required: sequencing_platform

To get past this error, I had to remove the dash "-" in front of nanopore-corrected:

${GALA} ${DRAFTS} fq ${READS} nanopore-corrected

That got it past that error, but I am currently dealing with Minimap2 now yelling about something, which I will diagnose and report back on.

Speaking to that error though, it seems to me that the syntax guidance on the frontpage of this github repo says to use the following for sequence platforms:

-pacbio-raw -pacbio-corrected -nanopore-raw -nanopore-corrected

...yet that front dash causes a problem.

So perhaps the syntax guidance needs changing, or the argparse code regarding this positional argment.

Best,

John Urban