Incomplete Documentation regarding expected outputs

[VasLem]

There is nowhere in the website, or the docs, information about the output of each step. I am currently developing a pipeline and I want to know the exact output that I expect from each step. Please update the documentation.

[FelixKrueger]

Hmm, I am not quite sure I agree... The documentation is here: https://felixkrueger.github.io/Bismark/

And here is an example. Is there anything specific you are referring to?

[VasLem]

Hi, thanks for the quick reply. Indeed there exists quite extensive documentation for the files produced by bismark_methylation_extractor, as well as the format of the bam files. However documentation is missing for the outputs of:

• bismark_genome_preparation
• bismark
• deduplicate_bismark

Given that the output filenames are pretty much constant, they should be documented somewhere. For example, bismark_genome_preparation is creates a folder Bisulfite_Genome, which then is populated by two subfolders with known names. This information resides only in the code.

[FelixKrueger]

I went had a look at the docs, and decided to add in a few bits and pieces (as well as update some out-of date things...).

Here are some additional notes for the output of Bismark. Here I added a new document for the options of the deduplication part. And finally fleshed out the section for the genome preparation.

Can you take a look and see if you are a bit more happy with this?

[VasLem]

Nice, yes, now it is clear! Thanks for the quick updates! :)

[VasLem]

I noticed that the output files names are also missing from here, can you update that part as well?

[FelixKrueger]

I have added some examples as well now. Good luck!