First adaptations.

Author: vinjana

resources/analysisTools/qcPipeline/environments/tbi-lsf-cluster.sh

@@ -129,16 +129,32 @@ export -f sambamba_markdup
 export SAMBAMBA_MARKDUP_BINARY=sambamba_markdup
 
 
+# Try to infer the module name and binary filename from the version number.
+bwaMajorVersion="$(echo "$BWA_VERSION" | cut -f 1 -d '.')"
+if [[ "$bwaMajorVersion" == "0" ]]; then
+  export BWA_MODULE=bwa
+elif [[ "$bwaMajorVersion" == "2" ]]; then
+  export BWA_MODULE=bwa-mem2
+else
+  echo "Cannot infer BWA_MODULE and BWA_BINARY from BWA_VERSION: '$BWA_VERSION'" >> /dev/stderr
+  exit 1
+fi
+
 if [[ "$WORKFLOW_ID" == "bisulfiteCoreAnalysis" ]]; then
+    if [[ "$bwaMajorVersion" != "1" ]]; then
+      echo "Only bwa-0.* has a bisulfite patch module" >> /dev/stderr
+      exit 1
+    fi
     ## For bisulfite alignment, we suffix the the value of BINARY_VERSION by '-bisulfite', because that's the name in LSF cluster.
     export BWA_VERSION="${BWA_VERSION:?BWA_VERSION is not set}-bisulfite"
-    moduleLoad bwa
-    export BWA_BINARY=bwa
+    # This works with BWA_MODULE because the bwa-mem2 binary has the same interface.
+    moduleLoad "$BWA_MODULE" BWA_VERSION
+    export BWA_BINARY="$BWA_MODULE"
 
 elif [[ "$WORKFLOW_ID" == "qcAnalysis" || "$WORKFLOW_ID" == "exomeAnalysis" ]]; then
     if [[ "${useAcceleratedHardware:-false}" == false ]]; then
-        moduleLoad bwa
-        export BWA_BINARY=bwa
+        moduleLoad "$BWA_MODULE" BWA_VERSION
+        export BWA_BINARY="$BWA_MODULE"
     elif [[ "${useAcceleratedHardware:-true}" == true ]]; then
         moduleLoad bwa-bb BWA_VERSION
         export BWA_ACCELERATED_BINARY=bwa-bb

resources/configurationFiles/analysisQC.xml

@@ -30,7 +30,11 @@
         <cvalue name="BIOBAMBAM_VERSION" value="0.0.148" type="string"/>
         <cvalue name="JAVA_VERSION" value="1.8.0_131" type="string"/>
         <cvalue name="BWA_VERSION" value="0.7.8" type="string"
-                description="Use e.g. 0.7.8-r2.05 for a specific revision of bb-bwa."/>
+                description="Use e.g. 0.7.8-r2.05 for a specific revision of bb-bwa. Node that bwa-mem2 uses much more memory."/>
+        <cvalue name="BWA_MODULE" value="" type="string"
+                description="Empty string will result in automatic inference of the module name. If the first number (major version) is '2' then BWA_MODULE is automatically set to 'bwa-mem2', otherwise 'bwa'. See tbi-lsf-cluster.sh. You can also explicitly set the version."/>
+        <cvalue name="BWA_MEM_OPTIONS" value='" -T 0 "' type="string"
+                description="The original CO configuration is ' -T 0 '. Note that  the value must be quoted."/>
         <cvalue name="FASTQC_VERSION" value="0.11.3" type="string"/>
 
         <cvalue name="workflowEnvironmentScript" value="workflowEnvironment_tbiLsf" type="string"/>