fix: bwa-mem options usage

CCBR · Oct 24, 2023 · ca4f84b · ca4f84b
1 parent 432ebfc
commit ca4f84b
Showing 1 changed file with 5 additions and 1 deletion.
diff --git a/modules/CCBR/bwa/mem/main.nf b/modules/CCBR/bwa/mem/main.nf
@@ -25,7 +25,11 @@ process BWA_MEM {
 
     INDEX=`find -L ./ -name "*.amb" | sed 's/\\.amb\$//'`
 
-    bwa mem -t ${task.cpus} \$INDEX ${fastq} -o \$TMP/align.bam
+    bwa mem \\
+      -t ${task.cpus} \\
+      -o \$TMP/align.bam \\
+      \$INDEX \\
+      ${fastq}
 
     samtools sort \\
       -@ ${task.cpus} \\