From 0b2a16c2e851c6a636bddb01ab99a9860d14fb7f Mon Sep 17 00:00:00 2001
From: Sergey Koren <sergek@umd.edu>
Date: Fri, 22 Dec 2023 17:10:26 -0500
Subject: [PATCH] fix threading when there's only 1 core

---
 src/Snakefiles/c4-findErrors.sm | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/src/Snakefiles/c4-findErrors.sm b/src/Snakefiles/c4-findErrors.sm
index 44ecd451..403de47e 100644
--- a/src/Snakefiles/c4-findErrors.sm
+++ b/src/Snakefiles/c4-findErrors.sm
@@ -92,7 +92,11 @@ rule computeErrors:
 cd       0-correction/find-errors-jobs
 
 range=`cat ../../{input.range}`
-ncpus=`expr {threads} - 1`          #  One CPU is used for I/O.
+if [ {threads} -gt 1 ]; then
+   ncpus=`expr {threads} - 1`          #  One CPU is used for I/O.
+else
+   ncpus={threads}
+fi
 
 cat > ./{wildcards.nnnn}.sh <<EOF
 #!/bin/sh