Add hifiasm for long reads assemble

[scintilla9]

Hi Dr Almeida,

Thank you for the detailed genome assembly workflow. Could you please include another assembler, hifiasm(https://github.com/chhylp123/hifiasm)? It is particularly suited for long-read data

Best
Chia-Wei

[fmalmeida]

@scintilla9 ,
Sure thing. I think it has been on my plate for some time. I you work on including it for v3.2 which is currently being tested in dev branch.

[scintilla9]

Hi @fmalmeida

I would like to work on it recently.
And I noticed that when building environment on my local machine with Dockerfile in dev, the building process will fail due to the url for downloading busco database is no available.

[fmalmeida]

Hi @scintilla9 ,
Thanks for wanting to help with this.
And yes, the resources of it were deleted. I faced the same when trying to work on another issue (#50).
Basically, I have it fixed but not merged to dev yet as I did not finish its implementation yet ( I am changing to do the BUSCO run manually instead of by Quast).

So, for you to start working on this one, I would recommend creating a branch from the branch: 50-add-skip-parameter-for-sreads-polishers-and-fix-multiqc-report-names

Are you working on your own fork? If so, would need to "sync" the fork with mine, to have this branch in your repo so that you can create a branch from it.

Otherwise, I can create the branch for you in this repo.

[scintilla9]

Thanks for the information.
I have created my own fork, and will let you know if I got any questions.

[fmalmeida]

Hi @scintilla9 ,
I merged the code to the dev branch. As said in the PR, I will start the full dataset testings to guarantee I can make a new release.
Also, I opened a follow-up ticket now that hifiasm is available: #71
Many thanks for the contribution.