[x] Allow workflows to be specified from the config.yml.
[x] make all workflow targets explicit. No include and target anymore, just a list of rules for each workflow
[x] require users to specify rules/workflows using the elvers_workflows key.
[x] generate all output files within elvers main
[x] generate all input files within elvers main, based on input_options in the config
[x] simplify input_options. Currently repetitive across rules. Perhaps categories (raw reads, trimmed reads, etc are best? The actual directories and extensions can be stored in a defaults style file, which we could pull from when generating inputs.
punted from previous PR:
[x] Allow workflows to be specified from the config.yml.
[x] make all workflow targets explicit. No
includeandtargetanymore, just a list of rules for each workflow[x] require users to specify rules/workflows using the
elvers_workflowskey.[x] generate all output files within elvers main
[x] generate all input files within elvers main, based on input_options in the config
[x] simplify
input_options. Currently repetitive across rules. Perhaps categories (raw reads, trimmed reads, etc are best? The actual directories and extensions can be stored in adefaultsstyle file, which we could pull from when generating inputs.