novo lication

tasks/novoalign.wdl

@@ -13,7 +13,7 @@ task novoalign {
 		set -o pipefail
 		set -e	
 		nt=$(nproc)
-		novoalign -d ${NVref_dir}/${index} -f ${fastq_1} ${fastq_2} -o SAM -c $nt > ${sample}.novoalign.sam
+		/opt/novoalign -d ${NVref_dir}/${index} -f ${fastq_1} ${fastq_2} -o SAM -c $nt > ${sample}.novoalign.sam
 	>>>
 
 	runtime {