From dc3aae032aa2b12c8b59458e4244b3e06ff8bd4a Mon Sep 17 00:00:00 2001
From: Matin Nuhamunada <matinnu@biosustain.dtu.dk>
Date: Mon, 6 May 2024 12:20:14 +0000
Subject: [PATCH] fix: add parameters setting to change MASH sketch size

---
 workflow/rules/mash.smk | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/workflow/rules/mash.smk b/workflow/rules/mash.smk
index 814a24ec..106aacb3 100644
--- a/workflow/rules/mash.smk
+++ b/workflow/rules/mash.smk
@@ -7,6 +7,8 @@ rule mash:
     conda:
         "../envs/mash.yaml"
     threads: 32
+    params:
+        sketch_size=1000,
     log:
         "logs/mash/mash-triangle-{name}.log",
     shell:
@@ -15,7 +17,7 @@ rule mash:
         do
             echo $fna >> {output.mash_infile}
         done
-        (mash triangle -p {threads} -l {output.mash_infile} >> {output.triangle_dist}) 2>> {log}
+        (mash triangle -s {params.sketch_size} -p {threads} -l {output.mash_infile} >> {output.triangle_dist}) 2>> {log}
         """