From 28ea61014d5d88a566ed14e4849e1b42430b7cc4 Mon Sep 17 00:00:00 2001
From: "C. Titus Brown" <titus@idyll.org>
Date: Sat, 15 Jan 2022 05:50:56 -0800
Subject: [PATCH] add picklists into the config (#136)

---
 conf-private.yml            | 2 ++
 genome_grist/conf/Snakefile | 4 +++-
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/conf-private.yml b/conf-private.yml
index 69d7561..e970750 100644
--- a/conf-private.yml
+++ b/conf-private.yml
@@ -13,3 +13,5 @@ private_databases_info:
 
 taxonomies:
 - databases/podar-ref.tax.csv
+
+picklist: xyz.csv::manifest
diff --git a/genome_grist/conf/Snakefile b/genome_grist/conf/Snakefile
index 5bf165f..f4761cd 100755
--- a/genome_grist/conf/Snakefile
+++ b/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