Update: samtools dir

tasks/replaceRG.wdl

@@ -10,8 +10,9 @@ task replaceRG {
   String disk_size
 
   command <<<
-    samtools addreplacerg -r "@RG\tID:${group}\tSM:${sample}\tPL:${pl}" -o ${bam_name}.bam ${bam}
-    samtools index ${bam_name}.bam
+    SAMTOOLS_DIR="/opt/samtools/samtools-1.13"
+    $SAMTOOLS_DIR/samtools addreplacerg -r "@RG\tID:${group}\tSM:${sample}\tPL:${pl}" -o ${bam_name}.bam ${bam}
+    $SAMTOOLS_DIR/samtools index ${bam_name}.bam
   >>>
 
   runtime {