- Moved constructor to function itself

- Add extract option to fastqc

flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Fastqc.scala

@@ -18,13 +18,14 @@ class Fastqc(val root: Configurable) extends BiopetCommandLineFunction {
 
   @Output(doc = "Output", shortName = "out")
   var output: File = _
-
+  
   executable = config("exe", default = "fastqc")
   var java_exe: String = config("exe", default = "java", submodule = "java")
   var kmers: Option[Int] = config("kmers")
   var quiet: Boolean = config("quiet")
   var noextract: Boolean = config("noextract")
   var nogroup: Boolean = config("nogroup")
+  var extract: Boolean = config("extract", default = true)
 
   override val versionRegex = """FastQC (.*)""".r
   override val defaultThreads = 4
@@ -45,9 +46,24 @@ class Fastqc(val root: Configurable) extends BiopetCommandLineFunction {
       optional("--kmers", kmers) +
       conditional(nogroup, "--nogroup") +
       conditional(noextract, "--noextract") +
+      conditional(extract, "--extract") +
       conditional(quiet, "--quiet") +
       required("-o", output.getParent()) +
-      required(fastqfile) +
-      required(" > ", output, escape = false)
+      required(fastqfile)
   }
 }
+
+object Fastqc {
+  def apply(root:Configurable, fastqfile: File, outDir: String): Fastqc = {
+    val fastqcCommand = new Fastqc(root)
+    fastqcCommand.fastqfile = fastqfile
+    var filename: String = fastqfile.getName()
+    if (filename.endsWith(".gz")) filename = filename.substring(0, filename.size - 3)
+    if (filename.endsWith(".gzip")) filename = filename.substring(0, filename.size - 5)
+    if (filename.endsWith(".fastq")) filename = filename.substring(0, filename.size - 6)
+    //if (filename.endsWith(".fq")) filename = filename.substring(0,filename.size - 3)
+    fastqcCommand.jobOutputFile = new File(outDir + "/" + filename + "_fastqc.zip")
+    fastqcCommand.afterGraph
+    return fastqcCommand
+  }
+}
\ No newline at end of file

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

@@ -81,13 +81,13 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
     addSha1sum(outputFiles("fastq_input_R1"), "sha1_R1")
     if (paired) addSha1sum(outputFiles("fastq_input_R2"), "sha1_R2")
 
-    var fastqc_R1 = runFastqc(input_R1, outputDir + "/" + R1_name + ".fastqc/")
+    var fastqc_R1 = Fastqc(this, input_R1, outputDir + "/" + R1_name + ".fastqc/")
     outputFiles += ("fastqc_R1" -> fastqc_R1.output)
     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 + "/" + R2_name + ".fastqc/")
+      var fastqc_R2 = Fastqc(this, input_R2, outputDir + "/" + R2_name + ".fastqc/")
       outputFiles += ("fastqc_R2" -> fastqc_R2.output)
       outputFiles += ("qualtype_R2" -> getQualtype(fastqc_R2, R2_name))
       outputFiles += ("contams_R2" -> getContams(fastqc_R2, R2_name))
@@ -226,9 +226,9 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
 
       addSha1sum(R1, "sha1_qc_R1")
       if (paired) addSha1sum(R2, "sha1_qc_R2")
-
-      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)
+      
+      outputFiles += ("fastqc_R1_final" -> Fastqc(this, outputFiles("output_R1"), outputDir + "/" + R1_name + ".qc.fastqc/").output)
+      if (paired) outputFiles += ("fastqc_R2_final" -> Fastqc(this, outputFiles("output_R2"), outputDir + "/" + R2_name + ".qc.fastqc/").output)
     }
 
     if (!skipSummary) {
@@ -245,20 +245,6 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
     }
   }
 
-  def runFastqc(fastqfile: File, outDir: String): Fastqc = {
-    val fastqcCommand = new Fastqc(this)
-    fastqcCommand.fastqfile = fastqfile
-    var filename: String = fastqfile.getName()
-    if (filename.endsWith(".gz")) filename = filename.substring(0, filename.size - 3)
-    if (filename.endsWith(".gzip")) filename = filename.substring(0, filename.size - 5)
-    if (filename.endsWith(".fastq")) filename = filename.substring(0, filename.size - 6)
-    //if (filename.endsWith(".fq")) filename = filename.substring(0,filename.size - 3)
-    fastqcCommand.output = outDir + "/" + filename + "_fastqc.output"
-    fastqcCommand.afterGraph
-    add(fastqcCommand)
-    return fastqcCommand
-  }
-
   def extractIfNeeded(file: File, runDir: String): File = {
     if (file.getName().endsWith(".gz") || file.getName().endsWith(".gzip")) {
       var newFile: File = swapExt(runDir, file, ".gz", "")