ingest: add species config param

Add ability to configure species so that users can run ingest for a
subset of species. Motivated by discussion in
<#56 (comment)>

Author: joverlee521

ingest/Snakefile

@@ -8,7 +8,7 @@ workdir: workflow.current_basedir
 # Use default configuration values. Override with Snakemake's --configfile/--config options.
 configfile: "defaults/config.yaml"
 
-SPECIES = ['ebov', 'bdbv', 'sudv']
+SPECIES = config["species"]
 
 # This is the default rule that Snakemake will run when there are no specified targets.
 # The default output of the ingest workflow is usually the curated metadata and sequences.

ingest/defaults/config.yaml

@@ -3,6 +3,10 @@
 #
 # Define optional config parameters with their default values here so that users
 # do not have to dig through the workflows to figure out the default values
+species:
+  - ebov
+  - bdbv
+  - sudv
 
 ppx_fetch:
   ebov: # zaire