add sourmash_database_threshold_bp to docs, config check (#162)

dib-lab · Feb 12, 2022 · d913235 · d913235
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diff --git a/doc/configuring.md b/doc/configuring.md
@@ -341,6 +341,12 @@ prevent_sra_download: false
 #     picklist: some_sig_list.csv:ident:ident
 picklist: ""
 
+# sourmash_database_threshold_bp: sets the --threshold-bp minimum match
+# size of sourmash prefetch and gather. This will exclude matches with
+# smaller overlaps than this from being considered.
+# DEFAULT: 1e5
+sourmash_database_threshold_bp: 10000
+
 # sourmash_database_ksize: k-mer size to use when searching sourmash databases.
 # DEFAULT: 31
 sourmash_database_ksize: 31

diff --git a/genome_grist/conf/Snakefile b/genome_grist/conf/Snakefile
@@ -99,6 +99,7 @@ known_config_keys = { 'samples', 'outdir', 'tempdir',
                       'genbank_cache',
                       'sourmash_databases',
                       'local_databases_info',
+                      'sourmash_database_threshold_bp',
                       'sourmash_database_ksize',
                       'sourmash_compute_ksizes',
                       'sourmash_scaled',