Progress report

[Diaz335]

@jelmerp

[jelmerp]

Aspect	Max. points	Your points
Scripts	4	3	Your script is not yet well-developed, it is more of a collection of workflow progress notes with commands.[1]
Overview of scripts	3	2	The overview is a bit general and vague[2] and you didn't mention how you aim to tie things together, e.g. with a bash script or Snakemake.
To-do list	1.5	1	Comparing your plans in the General_Description.md and your current script, the to-do list seems too short and low on detail.
Git commits	1.5	1.5
Late submission with no notice	N/A	-1
TOTAL	10	6.5

^[1] Such a description, including installation procedures, is really helpful, but you'll want to end up separating installation from the actual running of the workflow. I also had to go click on each file to find the one that is a script, with no clear indication in the README or an appropriate file extension. ^[2] I would have liked to see a clearer overview of what script will do what, especially since right now, everything is just a series of commands in a single markdown file.

Some other comments:

• Your extracting_from_soybase.md and vision.md files render really poorly on GitHub (take a look at it to see what I mean), e.g. with linebreaks ignored like Markdown does. As they currently are, they would be better with a .sh extension, or you could reformat to proper Markdown.

• Let me know if you keep having troubles with VCF-to-BED conversion, I should be able to help with that. Alternatively, this could be a good coding exercise with awk or Python.