Improvements in download module, merging folders in sftp and log_summary implementation

[Shettland]

This pull request has two main objectives.

The first one is to provide the first steps to close #245. For this task, i implemented two small methods (update_summary and create_error_summary) to generate a custom log file in json format using two auxiliar methods (include_error and include_warning) several times along the code which will be emailed to the user after execution.
This first approach might be developed further into a new module which will create the same custom log summary for the rest of the modules in the tools.

The second one is a big enhancement on the code that aims to help this previously mentioned task by merging all the remote subfolders in the sftp repository with batches of samples and metadata from each user into a single one, so each user receives only one single report instead of one for each batch of samples.

[saramonzon]

Good job! Some minor comments, and a suggestion about how to avoid using log for including sample-based error. I think if the problem is that you don't have the sample_name and only the filename it's easy to create a self.sample_files dict with this information, as this is the json you are going to print as output, and use it when you need it to include the errors. If I'm not mistaken you can use a list comprenhension to add the error to all corrupted files in the list.