removes spaces

UPHL-BioNGS · Apr 24, 2024 · 84c195a · 84c195a
1 parent 9a78ae3
commit 84c195a
Showing 1 changed file with 2 additions and 1 deletion.
diff --git a/modules/local/mlst.nf b/modules/local/mlst.nf
@@ -25,7 +25,8 @@ process mlst {
 
     mlst ${args} \
       --threads ${task.cpus} \
-      ${contig} \
+      ${contig} | \
+      tr ' ' '_' \
       > ${prefix}_mlst.txt
 
     python3 ${script} ${prefix}_mlst.txt mlst/${prefix}_mlst.tsv mlst ${prefix}