BioX::Workflow::Writer::Drake - A very opinionated template based bioinformatics workflow wr

[Jillian Rowe]

Hi Drake team,

I really, really like using drake, and I wrote a wrapper in perl around drake that takes a workflow defined in a config file an writes out the drake output. It is designed for bioinformatics/genomics workflows, meaning you are running many samples through the exact same sequence of commands. There are many options for finding samples, creating rules, and creating a structured output.

Here's the page for the listing of documentation: BioX-Workflow

Thanks for all the work that went into drake!

Acknowledgements

This module was originally developed at and for Weill Cornell Medical College in Qatar within ITS Advanced Computing Team. With approval from WCMC-Q, this information was generalized and put on github, for which the authors would like to express their gratitude.

Best,
Jillian

[Artem Boytsov]

Hello Julian,

This looks pretty cool. And well documented too! 

Thank you for this work and your kind words - I am personally very excited about Drake's continued (albeit slow) adoption. Thus far, the tutorial video has been watched for ~233 hours, the repo's got 890 stars and 62 forks, and the first page of Google results for "drake workflow" or "drake data" are all about Drake (hard to compete with Drake Graham!). 

Even though it may look modest by comparison to some other tools, it does not diminish in the slightest all the hard work that went into Drake - most of it by the Clojurians at Factual, who not only continue to maintain and develop Drake, but also use it in-house. You guys are really great!

Yours,

  Artem.

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Yours,
  Artem.

[Jillian Rowe]

Hi Artem,

Thanks, I strive for decent documentation. ;)

I prefer that drake be simple and text based. I think a lot of workflow managers over complicate things when all I want is a directed graph, and force you to add on all kinds of work. No one wants to learn java/python/whatever to run a single job. I can't tell you how many times drake has saved me from rerunning an entire workflow, because it tells me "hey stupid you already ran that!". 

What are the future plans for drake?

Best,

Jilian

[Artem Boytsov]

This question would be better answered by the brave folk at Factual, specifically Alan Malloy (CC-ed) who owns the Drake codebase now.

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Yours,
  Artem.

[Aaron Crow]

Hi Jillian, thanks for the kind words. I can't say there's anything like a clear, "master roadmap" for Drake. There's the detailed spec that Artem headed up, which has plenty of un-done features described. Beyond that, we'll (a) upgrade and fix Drake on a case-by-case basis, (b) happily review pull requests, and (c) consider all other feedback & bug reports as they come in.

If you have any specific feedback or suggestions for us (e.g., "don't add that feature, it'll make things too complicated!")... please feel free to file a ticket or shoot us an email.

All the best,

Aaron

[Jillian Rowe]

Hi Aaron,

I can't think of any features I would like added, but I would love to see a complete example with a log4j appender.

Best,
Jillian