Get Data Utility Rule

To run any workflow, we need to get reads (and any assemblies already generated) into the right format for elvers. We can either (1) link the data from another location on your machine, or (2) download the data via http or ftp. This is done through a utility rule called get_data.

At the moment, get_data only works with gzipped files. Checks and improved functionality coming soon

Modifying Params for get_data:

Be sure to set up your sample info and build a configfile first (see Understanding and Configuring Workflows).

To see the available parameters for the get_data utility rule, run

elvers config get_data --print_params

In here, you'll see a section for "get_data" parameters that looks like this:

  ####################  get_data  ####################
get_data:
  download_data: false
  use_ftp: false
  #####################################################

If you want to download data, you'll want to change the download_data and use_ftp parameters appropriately. To download via http, set download_data: True. To download via ftp, set download_data: True and use_ftp: True.

Output Files

The output of the get_data step is all your input data files in a subdirectory (input_data) within your output directory (basename_out). These will either be links or downloaded files, depending on the options you specified in the config file.