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ewels / clusterflow

A pipelining tool to automate and standardise bioinformatics analyses on cluster environments.
https://ewels.github.io/clusterflow/
GNU General Public License v3.0
97 stars 27 forks source link

The great BI merge of 2016 #88

Closed ewels closed 8 years ago

ewels commented 8 years ago

Ok, I'm gearing up to release v0.4 of Cluster Flow, this v0.4dev madness has gone on for long enough. So, time to try to bring in all of your new code.

The PR below looks relatively sensible, main problem is the new modules that still use the old syntax for requesting resources. They won't work with the current CF code. I can update them so that they do, but then I'd really like you guys to start using the newly released v0.4 version so we don't have to do this again ;)

Sounds doable?

ewels commented 8 years ago

ps. Other pet hate is leaving commented out code in the package, so I'll probably delete that too if that's ok.

ewels commented 8 years ago

Ok, so proposed workflow:

  1. I merge this PR into a new branch on my repository
  2. I do my own updates there to make the code compatible with current version of cluster flow
  3. I do a branch PR back into master and you guys can look over what I've done
  4. I release v0.4
  5. You guys merge new v0.4 code into your repo
  6. You guys actually use v0.4 :)

Sound ok @s-andrews @FelixKrueger?

s-andrews commented 8 years ago

Sure - works for me. Would be good to try the new repo as soon as you have it merged - I'd still like to get some of the file naming issues sorted out before a final 0.4 release so we don't end up working off a branch again.

Simon.

ewels commented 8 years ago

Ok, I finished sorting out all of the merge conflicts. See commit 82afc086014c3d9269488f53e4d1dc264403bfb4

I admit I thought that this would then class this PR as merged, but apparently not. Maybe I have to merge your commits into master for that.

Anyway, I will do some more updating on that branch and then merge into master when I'm happy.