Writing your first paper is a real important topic. I've recently come across a nice article by Jeff Leek who explains this topic in a really straight forward way here. In this blog post I am trying to summarize the main points mostly to be used as a note reference to myself. Jeff brakes it down into concrete steps as part of a project. He starts by describing its characteristics:

1. It should be concrete
2. Should solve a scientific problem
3. Gives you the opportunity to learn something new
4. Something you feel ownership of
5. Something you want to work on

Having defined your problem next step is actually conducting the research. Here Jeff suggests following the usual data analytic process:

1. Define the question
2. Get/tidy the data
3. Explore the data
4. Build/borrow a model
5. Perform the analysis
6. Critique the results
7. Write the paper

As Jeff points out the hardest part is knowing where to stop and start writing.

Don't strive for perfection not at least in the beginning! After all a published paper is better than a non published one.

A result worth reporting ususally takes the form of between 1-5 figures showing a coherent story that you could explain to someone in your field.

In a sense these are the steps involved in writing a paper:

1. Create 1-4 publication quality plots
2. Write a story in the simplest language for the plots while still reporting all the technical details
3. Add references only after you have finished the whole first draft
4. Add in additional technical detail in the supplementary material if needed be
5. Write up a reproducible version of your code that returns the exactly same numbers/figures in your paper with no input parameters needed