Change name

public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/CheckMd5.scala → public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/CheckChecksum.scala

@@ -11,26 +11,26 @@ import org.broadinstitute.gatk.utils.commandline.{ Argument, Input }
  *
  * Created by pjvanthof on 16/08/15.
  */
-class CheckMd5 extends InProcessFunction {
+class CheckChecksum extends InProcessFunction {
   @Input(required = true)
   var inputFile: File = _
 
   @Input(required = true)
-  var md5file: File = _
+  var checksumFile: File = _
 
   @Argument(required = true)
-  var md5sum: String = _
+  var checksum: String = _
 
   override def freezeFieldValues(): Unit = {
     super.freezeFieldValues()
-    jobOutputFile = new File(md5file.getParentFile, md5file.getName + ".check.out")
+    jobOutputFile = new File(checksumFile.getParentFile, checksumFile.getName + ".check.out")
   }
 
   /** Exits whenever the input md5sum is not the same as the output md5sum */
   def run: Unit = {
-    val outputMd5sum = WriteSummary.parseChecksum(md5file).toLowerCase
+    val outputChecksum = WriteSummary.parseChecksum(checksumFile).toLowerCase
 
-    if (outputMd5sum != md5sum.toLowerCase) {
+    if (outputChecksum != checksum.toLowerCase) {
       logger.error(s"Input file: '$inputFile' md5sum is not as expected, aborting pipeline")
       System.exit(1)
     }

public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala

@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.core.summary
 import java.io.File
 
 import nl.lumc.sasc.biopet.core._
-import nl.lumc.sasc.biopet.core.extensions.{ CheckMd5, Md5sum }
+import nl.lumc.sasc.biopet.core.extensions.{ CheckChecksum, Md5sum }
 
 import scala.collection.mutable
 
@@ -119,11 +119,11 @@ trait SummaryQScript extends BiopetQScript { qscript =>
     for (inputFile <- inputFiles) {
       inputFile.md5 match {
         case Some(checksum) => {
-          val checkMd5 = new CheckMd5
+          val checkMd5 = new CheckChecksum
           checkMd5.inputFile = inputFile.file
           require(SummaryQScript.md5sumCache.contains(inputFile.file), "Md5 job is not executed, checksum file can't be found")
-          checkMd5.md5file = SummaryQScript.md5sumCache(inputFile.file)
-          checkMd5.md5sum = checksum
+          checkMd5.checksumFile = SummaryQScript.md5sumCache(inputFile.file)
+          checkMd5.checksum = checksum
           add(checkMd5)
         }
         case _ =>