New assembler flag

[jpaganini]

Added new flag '-a' for specifying assembler tool. Only unicycler or spades are available.

If 'unicycler' is selected, coverage will not be used as a criteria for filtering potential contamination, since Unicycler already does a similar step.

[duboism]

I don't have an opinion on the utility of the modification from a bioinformatics point of view.

However, the current proposal breaks compatibility because the -a option is mandatory. It's not a problem per se but requires some thoughts on the versioning: keeping -a mandatory would require switching to version 2.0; another possibility is to use spades as the default value.

[duboism]

Also, we must update README.md to mention that PlaScope can now work with other assemblers.

[jpaganini]

Hi Mathieu,

I completely agree with using spades as default option in mode 2. I just modified that.

I also modified the README file.

Let me know if addtional modificaitons are required.

Cheers!

[jpaganini]

Hi guys,

Are you still considering merging this request? Would you like me to do any extra modification?

[duboism]

Hello,

Sorry for the delay. We discussed some ideas about your contribution but I think we will merge it as-this quickly. We just want to review the README.md file before doing a new version.

Just a little task for you: we have added a Contributors section in README.md; Could you merge master in your branch and add a line to describe your work in this section ?

[jpaganini]

Hi,

Thanks for the answer. I've been a bit busy myself lately. Modifications done!

[duboism]

Hello,

I can't see the commit(s) for your contribution. Did you push ?

[jpaganini]

Sorry! I havent! It should be present now!

[duboism]

Thanks !

@GuilhemRoyer : if you're OK, I can merge this.

[GuilhemRoyer]

Thanks !

@GuilhemRoyer : if you're OK, I can merge this.

Thank you @duboism, for sure I am Ok. Thank you also @jpaganini for your contribution.

[duboism]

I have merged the branch. Thanks @jpaganini ! I will release a new version as soon as we have decided for #5 .