Changed filenames for compatible summarize script

flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala

@@ -3,7 +3,6 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep
 import nl.lumc.sasc.biopet.core._
 import nl.lumc.sasc.biopet.wrappers._
 import org.broadinstitute.sting.queue.QScript
-import org.broadinstitute.sting.queue.engine.JobRunInfo
 import org.broadinstitute.sting.queue.extensions.gatk._
 import org.broadinstitute.sting.queue.extensions.picard._
 import org.broadinstitute.sting.queue.function._
@@ -21,8 +20,11 @@ class Flexiprep(private var globalConfig: Config) extends QScript with BiopetQSc
   @Argument(doc="Skip Trim fastq files", shortName="skiptrim", required=false) var skipTrim: Boolean = false
   @Argument(doc="Skip Clip fastq files", shortName="skipclip", required=false) var skipClip: Boolean = false
   
-  //var outputFiles:Map[String,File] = Map()
   var paired: Boolean = (input_R2 != null)
+  var R1_ext: String = _
+  var R2_ext: String = _
+  var R1_name: String = _
+  var R2_name: String = _
   
   def init() {
     for (file <- configfiles) globalConfig.loadConfigFile(file)
@@ -33,6 +35,20 @@ class Flexiprep(private var globalConfig: Config) extends QScript with BiopetQSc
     if (outputDir == null) throw new IllegalStateException("Missing Output directory on flexiprep module")
     else if (!outputDir.endsWith("/")) outputDir += "/"
     paired = (input_R2 != null)
+    
+    if (input_R1.endsWith(".gz")) R1_name = input_R1.getName.substring(0, input_R1.getName.lastIndexOf(".gz"))
+    else if (input_R1.endsWith(".gzip")) R1_name = input_R1.getName.substring(0, input_R1.getName.lastIndexOf(".gzip"))
+    else R1_name = input_R1
+    R1_ext = R1_name.substring(R1_name.lastIndexOf("."), R1_name.size)
+    R1_name = R1_name.substring(0, R1_name.lastIndexOf(R1_ext))
+    
+    if (paired) { 
+      if (input_R2.endsWith(".gz")) R2_name = input_R2.getName.substring(0, input_R2.getName.lastIndexOf(".gz"))
+      else if (input_R2.endsWith(".gzip")) R2_name = input_R2.getName.substring(0, input_R2.getName.lastIndexOf(".gzip"))
+      else R2_name = input_R2
+      R2_ext = R2_name.substring(R2_name.lastIndexOf("."), R2_name.size)
+      R2_name = R2_name.substring(0, R2_name.lastIndexOf(R2_ext))
+    }
   }
   
   def script() {
@@ -42,6 +58,12 @@ class Flexiprep(private var globalConfig: Config) extends QScript with BiopetQSc
     outputFiles += ("output_R1" -> zcatIfNeeded(input_R1,outputDir))
     if (paired) outputFiles += ("output_R2" -> zcatIfNeeded(input_R2,outputDir))
     
+    addSeqstat(outputFiles("output_R1"), "seqstat_R1")
+    if (paired) addSeqstat(outputFiles("output_R2"), "seqstat_qc_R2")
+    
+    addSha1sum(outputFiles("output_R1"), "sha1_R1")
+    if (paired) addSha1sum(outputFiles("output_R2"), "sha1_R2")
+    
     var results: Map[String,File] = Map()
     if (paired) {
       results = runTrimClip(outputFiles("output_R1"), outputFiles("output_R2"), outputDir)
@@ -51,36 +73,36 @@ class Flexiprep(private var globalConfig: Config) extends QScript with BiopetQSc
       results = runTrimClip(outputFiles("output_R1"), outputDir)
       outputFiles += ("output_R1" -> results("output_R1"))
     }
-    runFinalFastqc()
+    runFinalize(List(outputFiles("output_R1")), List(outputFiles("output_R2")))
   }
   
   def runInitialFastqc() {
-    var fastqc_R1 = runFastqc(input_R1,outputDir + "/fastqc_R1/")
+    var fastqc_R1 = runFastqc(input_R1,outputDir + "/" + R1_name + ".fastqc/")
     outputFiles += ("fastqc_R1" -> fastqc_R1.output)
-    outputFiles += ("qualtype_R1" -> getQualtype(fastqc_R1))
-    outputFiles += ("contams_R1" -> getContams(fastqc_R1))
+    outputFiles += ("qualtype_R1" -> getQualtype(fastqc_R1, R1_name))
+    outputFiles += ("contams_R1" -> getContams(fastqc_R1, R1_name))
     
     if (paired) {
-      var fastqc_R2 = runFastqc(input_R2,outputDir + "/fastqc_R2/")
+      var fastqc_R2 = runFastqc(input_R2,outputDir + "/" + R2_name + ".fastqc/")
       outputFiles += ("fastqc_R2" -> fastqc_R2.output)
-      outputFiles += ("qualtype_R2" -> getQualtype(fastqc_R2))
-      outputFiles += ("contams_R2" -> getContams(fastqc_R2))
+      outputFiles += ("qualtype_R2" -> getQualtype(fastqc_R2, R2_name))
+      outputFiles += ("contams_R2" -> getContams(fastqc_R2, R2_name))
     }
   }
   
-  def getQualtype(fastqc:Fastqc): File = {
+  def getQualtype(fastqc:Fastqc, pairname:String): File = {
     val fastqcToQualtype = new FastqcToQualtype(config) {
       this.fastqc_output = fastqc.output
-      this.out = swapExt(outputDir, fastqc.fastqfile, "", ".qualtype.txt")
+      this.out = new File(outputDir + pairname + ".qualtype.txt")
     }
     add(fastqcToQualtype)
     return fastqcToQualtype.out
   }
   
-  def getContams(fastqc:Fastqc): File = {
+  def getContams(fastqc:Fastqc, pairname:String): File = {
     val fastqcToContams = new FastqcToContams(config) {
       this.fastqc_output = fastqc.output
-      this.out = swapExt(outputDir, fastqc.fastqfile, "", ".contams.txt")
+      this.out = new File(outputDir + pairname + ".contams.txt")
       this.contams_file = fastqc.contaminants
     }
     add(fastqcToContams)
@@ -92,12 +114,9 @@ class Flexiprep(private var globalConfig: Config) extends QScript with BiopetQSc
   }
   def runTrimClip(R1_in:File, R2_in:File, outDir:String) : Map[String,File] = {
     var results: Map[String,File] = Map()
-    
+
     var R1: File = new File(R1_in)
     var R2: File = new File(R2_in)
-    var R1_ext: String = R1.getName().substring(R1.getName().lastIndexOf("."), R1.getName().size)
-    var R2_ext: String = ""
-    if (paired) R2_ext = R2.getName().substring(R2.getName().lastIndexOf("."), R2.getName().size)
     
     if (!skipClip) { // Adapter clipping
       val cutadapt_R1 = new Cutadapt(config) {
@@ -119,9 +138,9 @@ class Flexiprep(private var globalConfig: Config) extends QScript with BiopetQSc
           this.input_start_fastq = cutadapt_R1.fastq_input
           this.input_R1 = cutadapt_R1.fastq_output
           this.input_R2 = cutadapt_R2.fastq_output
-          this.output_R1 = swapExt(outDir, R1, ".clip"+R1_ext, ".clipsync"+R1_ext)
-          this.output_R2 = swapExt(outDir, R2, ".clip"+R2_ext, ".clipsync"+R2_ext)
-          this.output_stats = swapExt(outDir, R1, ".clip"+R1_ext, ".clipsync.stats")
+          this.output_R1 = swapExt(outDir, R1, R1_ext, ".sync"+R1_ext)
+          this.output_R2 = swapExt(outDir, R2, R2_ext, ".sync"+R2_ext)
+          this.output_stats = swapExt(outDir, R1, R1_ext, ".sync.stats")
         }
         add(fastqSync)
         R1 = fastqSync.output_R1
@@ -151,11 +170,52 @@ class Flexiprep(private var globalConfig: Config) extends QScript with BiopetQSc
     return results
   }
   
-  def runFinalFastqc() {
+  def runFinalize(fastq_R1:List[File], fastq_R2:List[File]) {
+    if (fastq_R1.length != fastq_R2.length) throw new IllegalStateException("R1 and R2 file number is not the same")
+    var R1: File = ""
+    var R2: File = ""
+    if (fastq_R1.length == 1) { 
+      for (file <- fastq_R1) R1 = file
+      for (file <- fastq_R2) R2 = file
+    } else {
+      throw new IllegalStateException("Not yet inplemented") // For chuncking
+    }
+    
+    if (!config.getAsBoolean("skip_native_link", false)) {
+      val lnR1 = new Ln(config) { this.in = R1 }
+      R1 = new File(outputDir + R1_name + ".qc" + R1_ext)
+      lnR1.out = R1
+      add(lnR1)
+      if (paired) {
+        val lnR2 = new Ln(config) { this.in = R2 }
+        R2 = new File(outputDir + R2_name + ".qc" + R2_ext)
+        lnR2.out = R2
+        add(lnR2)
+      }
+    }
+    
+    addSeqstat(R1, "seqstat_qc_R1")
+    if (paired) addSeqstat(R2, "seqstat_qc_R2")
+    
+    addSha1sum(R1, "sha1_qc_R1")
+    if (paired) addSha1sum(R2, "sha1_qc_R2")
+    
     if (!skipTrim || !skipClip) {
-      outputFiles += ("fastqc_R1_final" -> runFastqc(outputFiles("output_R1"),outputDir + "/fastqc_qc_R1/").output)
-      if (paired) outputFiles += ("fastqc_R2_final" -> runFastqc(outputFiles("output_R2"),outputDir + "/fastqc_qc_R2/").output)
+      outputFiles += ("fastqc_R1_final" -> runFastqc(outputFiles("output_R1"),outputDir + "/" + R1_name + ".qc.fastqc/").output)
+      if (paired) outputFiles += ("fastqc_R2_final" -> runFastqc(outputFiles("output_R2"),outputDir + "/" + R2_name + ".qc.fastqc/").output)
+    }
+    
+    val summarize = new Summarize(config) {
+      this.runDir = outputDir
+      this.samplea = R1_name
+      if (paired) this.sampleb = R2_name
+      this.samplename = R1_name
+      this.clip = !skipClip
+      this.trim = !skipTrim
+      this.out = new File(outputDir + R1_name + ".summary.json")
     }
+    for ((k,v) <- outputFiles) summarize.deps +:= v
+    add(summarize)
   }
   
   def runFastqc(fastqfile:File, outDir:String) : Fastqc = {
@@ -183,8 +243,20 @@ class Flexiprep(private var globalConfig: Config) extends QScript with BiopetQSc
     } else return file
   }
   
-  override def onExecutionDone(jobs: Map[QFunction, JobRunInfo], success: Boolean) {
-    logger.info("Flexiprep is done")
+  def addSeqstat(fastq:File, key:String) {
+    val ext = fastq.getName.substring(fastq.getName.lastIndexOf("."))
+    val seqstat = new Seqstat(config) { this.input_fastq = fastq }
+    seqstat.out = swapExt(outputDir, fastq, ext, ".seqstats.json")
+    add(seqstat)
+    outputFiles += (key -> seqstat.out)
+  }
+  
+  def addSha1sum(fastq:File, key:String) {
+    val ext = fastq.getName.substring(fastq.getName.lastIndexOf("."))
+    val sha1sum = new Sha1sum(config) { this.in = fastq }
+    sha1sum.out = swapExt(outputDir, fastq, ext, ".sha1")
+    add(sha1sum)
+    outputFiles += (key -> sha1sum.out)
   }
 }