Formatting and typo corrections #1

[patrick-austin]

Minor changes to @leandro-liborio 's revisions:

• Typos
• Line lengths
• Removing some newlines from introduction slides - MD only interprets double newlines (singles are treated as whitespace) but this was forcing the image on the slides off the bottom of the page, and causing odd spaces in the middle of sentences
• Format MD hyperlink in intro slides
• Adding abbreviation expansions in some places
• Reverted change to the file name of one of the outputs, as it broke the MD formatting and the file names were chosen to match the outputs as they appear in Galaxy
• Changed two places where we still made references to using the .yaml file as an input to the workflow (we now run the yaml config tool in the first stage of the workflow instead)

The main (scientific) content should be unchanged.

[leandro-liborio]

Hi Patrick,

I think that all your changes are OK. Could not spot any problems.