tunning novoalign parameters

README.md

@@ -66,4 +66,8 @@ Parameters explanation
 
 `-o`  Specifies the report format
 
-`-c`  Sets the number of threads to be used. On licensed versions it defaults to the number of CPUs as reported by sysinfo(). On free version the option is disabled.
+`-c`  Sets the number of threads to be used. On licensed versions it defaults to the number of CPUs as reported by sysinfo(). On free version the option is disabled.
+
+##### Per sample running time
+
+to be added

tasks/novoalign.wdl

@@ -13,7 +13,7 @@ task novoalign {
 		set -o pipefail
 		set -e	
 		nt=$(nproc)
-		/opt/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 ­­--hlimit 9 ­-t 0,2 -c $nt > ${sample}.novoalign.sam
 	>>>
 
 	runtime {