[PRE REVIEW]: Sequana: a set of flexible genomic pipelines for processing and reporting NGS analysis

[whedon]

Submitting author: @cokelaer (Thomas Cokelaer)
Repository: https://github.com/sequana/sequana/
Version: 0.4.1
Editor: @pjotrp
Reviewer: @bow

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[arfon]

@pjotrp - the submitting author suggested you as a potential editor.

[pjotrp]

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[pjotrp]

@whedon assign @pjotrp as editor

[whedon]

OK, the editor is @pjotrp

[pjotrp]

@cokelaer thank you for your submission! I'll be looking for a reviewer soon. In the mean time can you help out with a few things? I can't find the paper.md and paper.bib files. Can you point them to me? Also can you make the LICENSE file standard - if it is it will show up on github with the right license icon. Thanks!

[cokelaer]

@ pjotrp
I've fixed the LICENSE and the icon now appears on github.
As for the paper.md and paper.bib, what do mean exactly ? Where shall I provide those files and what should be the content ? thanks

[pjotrp]

Best is to check one of the existing publication. See https://github.com/genenetwork/genenetwork2/tree/master/doc/joss/2016

[cokelaer]

Do the paper.bib and paper.md must be in the repository of the software or can they be put elsewhere ? Sequana is an organisation and we put the software in sequana/sequana but for papers, we'd like to keep it separate for instance in ./sequana/resources . Would it be fine with your policy ?

[arfon]

Would it be fine with your policy?

I think this is going to break some of our submission tooling (i.e. it's expected that the paper be in the software repository being reviewed). Let me check and get back to you.

For reference, some authors have made a folder in docs e.g..docs/paper/paper.md - might something like this work for you?

[pjotrp]

As the final paper gets generated from the source tree it is tied to the commit of that release. You can remove the paper from the source tree once it is published. It will be in that particular source release and git history. So it is not intrusive. Makes sense to tie it to the project, right?

[cokelaer]

okay, that's fine, I will add a ./joss directory in the ./doc
thanks

[cokelaer]

FYI we have added a paper.bib paper.md in https://github.com/sequana/sequana/tree/master/doc/joss

[pjotrp]

That looks great. @bow since since this is a snakemake application would you care to review this JOSS submission?

[bow]

@pjotrp & @cokelaer I'd be happy to review the submission. I would need a week's time, if that's ok.

[pjotrp]

No problem. Thanks @bow.

[pjotrp]

@whedon assign @bow as reviewer

[whedon]

OK, the reviewer is @bow

[pjotrp]

@whedon start review magic-word=bananas

[whedon]

OK, I've started the review over in #352. Feel free to close this issue now!