Add input files to pipelines

public/bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala

@@ -35,6 +35,7 @@ class Bam2Wig(val root: Configurable) extends QScript with BiopetQScript {
   var bamFile: File = null
 
   def init(): Unit = {
+    inputFiles :+= InputFile(bamFile)
   }
 
   def biopetScript(): Unit = {

public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala

@@ -71,7 +71,8 @@ class BamMetrics(val root: Configurable) extends QScript with SummaryQScript wit
   }
 
   /** executed before script */
-  def init() {
+  def init(): Unit = {
+    inputFiles :+= InputFile(inputBam)
   }
 
   /** Script to add jobs */

public/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/BastyTrait.scala

@@ -89,6 +89,8 @@ trait BastyTrait extends MultiSampleQScript {
     addAll(shiva.functions)
     addSummaryQScript(shiva)
 
+    inputFiles :::= shiva.inputFiles
+
     addSamplesJobs()
   }
 

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

@@ -21,6 +21,11 @@ class CheckMd5 extends InProcessFunction {
   @Argument(required = true)
   var md5sum: String = _
 
+  override def freezeFieldValues(): Unit = {
+    super.freezeFieldValues()
+    jobOutputFile = new File(md5file.getParentFile, md5file.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

public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala

@@ -78,6 +78,10 @@ class Carp(val root: Configurable) extends QScript with MultiSampleQScript with
         if (config.contains("R1")) {
           mapping.input_R1 = config("R1")
           if (config.contains("R2")) mapping.input_R2 = config("R2")
+
+          inputFiles :+= InputFile(mapping.input_R1, config("R1_md5"))
+          mapping.input_R2.foreach(inputFiles :+= InputFile(_, config("R2_md5")))
+
           mapping.init()
           mapping.biopetScript()
           addAll(mapping.functions)

public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala

@@ -844,6 +844,8 @@ class Gentrap(val root: Configurable) extends QScript
       def addJobs(): Unit = {
         // create per-library alignment file
         addAll(mappingJob.functions)
+        // Input file checking
+        inputFiles :::= mappingJob.inputFiles
         // add bigwig track
         addAll(bam2wigModule.functions)
         qscript.addSummaryQScript(mappingJob)

public/sage/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala

@@ -88,6 +88,8 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
       mapping.sampleId = Some(sampleId)
 
       protected def addJobs(): Unit = {
+        inputFiles :+= InputFile(inputFastq, config("R1_md5"))
+
         flexiprep.outputDir = new File(libDir, "flexiprep/")
         flexiprep.input_R1 = inputFastq
         flexiprep.init()

public/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala

@@ -35,6 +35,7 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
   var inputVCF: File = _
 
   def init(): Unit = {
+    inputFiles :+= InputFile(inputVCF)
   }
 
   override def defaults = ConfigUtils.mergeMaps(Map(