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flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepSummary.scala

 package nl.lumc.sasc.biopet.pipelines.flexiprep
 
 import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.function.Sha1sum
+import nl.lumc.sasc.biopet.function.fastq.Cutadapt
 import nl.lumc.sasc.biopet.function.fastq.Fastqc
+import nl.lumc.sasc.biopet.function.fastq.Sickle
+import nl.lumc.sasc.biopet.pipelines.flexiprep.scripts.FastqSync
+import nl.lumc.sasc.biopet.pipelines.flexiprep.scripts.Seqstat
 import org.broadinstitute.gatk.queue.function.InProcessFunction
-import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 import java.io.File
 import argonaut._, Argonaut._
 import scalaz._, Scalaz._
@@ -11,59 +16,59 @@ import scalaz._, Scalaz._
 class FlexiprepSummary(val root: Configurable) extends InProcessFunction with Configurable {
   this.analysisName = getClass.getSimpleName
 
-  @Input(doc = "Seq stat files R1", required=true)
-  var seqstatR1: List[File] = Nil
+  @Input(doc="deps")
+  var deps: List[File] = Nil
   
-  @Input(doc = "Seq stat files R2", required=false)
-  var seqstatR2: List[File] = Nil
-  
-  @Input(doc = "Seq stat files R1 after", required=false)
-  var seqstatR1after: List[File] = Nil
-  
-  @Input(doc = "Seq stat files R2 after", required=false)
-  var seqstatR2after: List[File] = Nil
-  
-  @Input(doc = "sha1 files R1", required=true)
-  var sha1R1: File = _
-  
-  @Input(doc = "sha1 files R2", required=false)
-  var sha1R2: File = _
+  @Output(doc = "Summary output", required=true)
+  var out: File = _
   
-  @Input(doc = "sha1 files R1 after", required=false)
-  var sha1R1after: File = _
+  class Chunk {
+    var seqstatR1: Seqstat = _
+    var seqstatR2: Seqstat = _
+    var seqstatR1after: Seqstat = _
+    var seqstatR2after: Seqstat = _
+    
+    var cutadaptR1: Cutadapt = _
+    var cutadaptR2: Cutadapt = _
+
+    var fastqSync: FastqSync = _
+
+    var sickle: Sickle = _
+  }
   
-  @Input(doc = "sha1 files R2 after", required=false)
-  var sha1R2after: File = _
+  var chunks: Map[String, Chunk] = Map()
   
-  @Input(doc = "Clip stat files R1", required=false)
-  var clipstatR1: List[File] = Nil
+  def addSeqstat(seqstat:Seqstat, R2:Boolean = false, after:Boolean = false, chunk:String=""): Seqstat = {
+    if (!chunks.contains(chunk)) chunks += (chunk -> new Chunk)
+    if (!R2 && !after) chunks(chunk).seqstatR1 = seqstat
+    else if (!R2 && after) chunks(chunk).seqstatR1after = seqstat
+    else if (R2 && !after) chunks(chunk).seqstatR2 = seqstat
+    else if (R2 && after) chunks(chunk).seqstatR2after = seqstat
+    deps ::= seqstat.out
+    return seqstat
+  }
   
-  @Input(doc = "Clip stat files R2", required=false)
-  var clipstatR2: List[File] = Nil
+  def addCutadapt(cutadapt:Cutadapt, R2:Boolean = false, chunk:String=""): Cutadapt = {
+    if (!chunks.contains(chunk)) chunks += (chunk -> new Chunk)
+    if (!R2) chunks(chunk).cutadaptR1 = cutadapt
+    else chunks(chunk).cutadaptR2 = cutadapt
+    //TODO: stats file of cutadapt
+    return cutadapt
+  }
   
-  @Input(doc = "Trim stat files", required=false)
-  var trimstats: List[File] = Nil
   
-  @Input(doc = "Sync stat files", required=false)
-  var syncstats: List[File] = Nil
   
-  @Output(doc = "Summary output", required=true)
-  var out: File = _
+  var sha1R1: Sha1sum = _
+  var sha1R2: Sha1sum = _
+  var sha1R1after: Sha1sum = _
+  var sha1R2after: Sha1sum = _
   
-  @Argument(doc = "fastqc files R1", required=true)
   var fastqcR1: Fastqc = _
-  
-  @Argument(doc = "fastqc files R2", required=false)
   var fastqcR2: Fastqc = _
-  
-  @Argument(doc = "fastqc files R1 after", required=false)
   var fastqcR1after: Fastqc = _
-  
-  @Argument(doc = "fastqc files R2 after", required=false)
   var fastqcR2after: Fastqc = _
   
-  @Argument(doc = "Flexiprep Pipeline", required=true)
-  var flexiprep: Flexiprep = _
+  var flexiprep: Flexiprep = root.asInstanceOf[Flexiprep]
   
   var clipping = true
   var trimming = true
@@ -74,58 +79,29 @@ class FlexiprepSummary(val root: Configurable) extends InProcessFunction with Co
     trimming = !flexiprep.skipTrim
     paired = flexiprep.paired
     
-    fastqcSummary(fastqcR1)
-    if (paired) fastqcSummary(fastqcR2)
-    
-    sha1Summary(sha1R1)
-    if (paired) sha1Summary(sha1R2)
-    
-    seqstatSummary(seqstatR1)
-    if (paired) seqstatSummary(seqstatR2)
-    
-    if (clipping) {
-      clipstatSummary(clipstatR1)
-      if (paired) {
-        clipstatSummary(clipstatR2)
-        syncstatSummary(syncstats)
-      }
-    }
-    
-    if (trimming) trimstatSummary(trimstats)
-    
-    if (clipping || trimming) {
-      fastqcSummary(fastqcR1after)
-      if (paired) fastqcSummary(fastqcR2after)
-      
-      sha1Summary(sha1R1after)
-      if (paired) sha1Summary(sha1R2after)
-      
-      seqstatSummary(seqstatR1after)
-      if (paired) seqstatSummary(seqstatR2after)
-    }
   }
   
-  def seqstatSummary(files: List[File]): Json = {
+  def seqstatSummary(): Json = {
     //TODO
     return null
   }
-  def sha1Summary(file:File): Json = {
+  def sha1Summary(): Json = {
     //TODO
     return null
   }
-  def fastqcSummary(fastqc:Fastqc): Json  = {
+  def fastqcSummary(): Json  = {
     //TODO
     return null
   }
-  def clipstatSummary(files: List[File]): Json = {
+  def clipstatSummary(): Json = {
     //TODO
     return null
   }
-  def syncstatSummary(files: List[File]): Json = {
+  def syncstatSummary(): Json = {
     //TODO
     return null
   }
-  def trimstatSummary(files: List[File]): Json = {
+  def trimstatSummary(): Json = {
     //TODO
     return null
   }