I am working on a ChIP-Seq pipeline in Snakemake

Question

I am working on a ChIP-Seq pipeline in Snakemake

endrebak opened this issue 7 years ago · comments

We are hoping to publish it as an applications note. Work in progress here:

https://github.com/biocore-ntnu/chip_seq_pipeline

Just a heads-up.

It is massive so reviewing it will probably be hard :/ Any feedback appreciated though :) Going to focus hard on finishing the docs and getting a beta out.

Edit: I see that I do not have an integration test, just plenty of dryrun tests testing the DAG logic. I started this before learning about this repo, so I might not be following best practices :/

Johannes Köster · Answer 1 · Tue Oct 10 2017 21:45:01 GMT+0800 (China Standard Time)

Great! I have only quickly scrolled through it so far. A first comment: it would be great if you could use wrappers for all tools like hisat2, epic and so on. This way, others can easily compose new workflows from these, and your code also becomes shorter. Finally, wrappers can be unit-tested.

Johannes Köster · Answer 2 · Wed Oct 09 2019 14:54:27 GMT+0800 (China Standard Time)

@endrebak what is the status of your chip-seq pipeline? Are you still planning to finalize it and include it into snakemake-workflows?

endrebak.ada · Answer 3 · Wed Oct 09 2019 15:07:35 GMT+0800 (China Standard Time)

Sorry, no. Have not worked on it for a while. It seemed hard to publish, so I focused on other stuff. Sorry for leaving this open. If sb. wants to create a new ChIP-Seq pipeline, I am available for discussions/PRs.