add picklists into the config (#136)

conf-private.yml

@@ -13,3 +13,5 @@ private_databases_info:
 
 taxonomies:
 - databases/podar-ref.tax.csv
+
+picklist: xyz.csv::manifest

genome_grist/conf/Snakefile

@@ -77,6 +77,7 @@ if config.get('database_taxonomy'):
     sys.exit(-1)
 
 TAXONOMY_DB = config.get('taxonomies', ["NO_TAXONOMIES_SPECIFIED_IN_CONFIG"])
+PICKLIST = config.get('picklist', '')
 
 # make a `sourmash sketch` -p param string.
 def make_param_str(ksizes, scaled):
@@ -822,13 +823,14 @@ rule sourmash_prefetch_wc:
         ksize = SOURMASH_DB_KSIZE,
         moltype = f"--{SOURMASH_COMPUTE_TYPE.lower()}",
         threshold_bp = SOURMASH_DATABASE_THRESHOLD_BP,
+        picklist = f"--picklist {PICKLIST}" if PICKLIST else ""
     shell: """
         echo "DB is {input.db}"
         sourmash prefetch {input.sig} {input.db} -k {params.ksize} \
           --threshold-bp={params.threshold_bp} {params.moltype} \
           --save-matching-hashes={output.known} \
           --save-unmatched-hashes={output.unknown} \
-          -o {output.csv}
+          {params.picklist} -o {output.csv}
     """
 
 # report on known and unknown hashes