Merge branch 'feature-option_keep_files_flexiprep' into 'develop'

Added a option to not keep the last fastq file anymore

See also #185 

Can not remove the zip action completely, it's still needed for the final fastqc. It's now intermediate by default when running flexiprep in an other pipeline on default.

See merge request !212

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

@@ -37,13 +37,19 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
   /** Skip Clip fastq files */
   var skipClip: Boolean = config("skip_clip", default = false)
 
+  /** Make a final fastq files, by default only when flexiprep is the main pipeline */
+  var keepQcFastqFiles: Boolean = config("keepQcFastqFiles", default = root == null)
+
   /** Location of summary file */
   def summaryFile = new File(outputDir, sampleId.getOrElse("x") + "-" + libId.getOrElse("x") + ".qc.summary.json")
 
   /** Returns files to store in summary */
   def summaryFiles: Map[String, File] = {
-    Map("input_R1" -> input_R1, "output_R1" -> outputFiles("output_R1_gzip")) ++
-      (if (paired) Map("input_R2" -> input_R2.get, "output_R2" -> outputFiles("output_R2_gzip")) else Map())
+    if (!skipTrim || !skipClip)
+      Map("input_R1" -> input_R1, "output_R1" -> outputFiles("output_R1_gzip")) ++
+        (if (paired) Map("input_R2" -> input_R2.get, "output_R2" -> outputFiles("output_R2_gzip")) else Map())
+    else Map("input_R1" -> input_R1) ++
+      (if (paired) Map("input_R2" -> input_R2.get) else Map())
   }
 
   /** returns settings to store in summary */
@@ -264,13 +270,13 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
     val R1 = new File(outputDir, R1_name + ".qc" + R1_ext + ".gz")
     val R2 = new File(outputDir, R2_name + ".qc" + R2_ext + ".gz")
 
-    add(Gzip(this, fastq_R1, R1))
-    if (paired) add(Gzip(this, fastq_R2, R2))
+    if (!skipTrim || !skipClip) {
+      add(Gzip(this, fastq_R1, R1), !keepQcFastqFiles)
+      if (paired) add(Gzip(this, fastq_R2, R2), !keepQcFastqFiles)
 
-    outputFiles += ("output_R1_gzip" -> R1)
-    if (paired) outputFiles += ("output_R2_gzip" -> R2)
+      outputFiles += ("output_R1_gzip" -> R1)
+      if (paired) outputFiles += ("output_R2_gzip" -> R2)
 
-    if (!skipTrim || !skipClip) {
       fastqc_R1_after = Fastqc(this, R1, new File(outputDir, R1_name + ".qc.fastqc/"))
       add(fastqc_R1_after)
       addSummarizable(fastqc_R1_after, "fastqc_R1_qc")

public/flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepTest.scala

@@ -84,7 +84,7 @@ class FlexiprepTest extends TestNGSuite with Matchers {
     flexiprep.functions.count(_.isInstanceOf[Cutadapt]) shouldBe (if (skipClip) 0 else if (paired) 2 else 1)
     flexiprep.functions.count(_.isInstanceOf[FastqSync]) shouldBe (if (skipClip) 0 else if (paired) 1 else 0)
     flexiprep.functions.count(_.isInstanceOf[Sickle]) shouldBe (if (skipTrim) 0 else 1)
-    flexiprep.functions.count(_.isInstanceOf[Gzip]) shouldBe (if (paired) 2 else 1)
+    flexiprep.functions.count(_.isInstanceOf[Gzip]) shouldBe (if (skipClip && skipTrim) 0 else if (paired) 2 else 1)
   }
 
   // remove temporary run directory all tests in the class have been run

public/pom.xml

@@ -154,6 +154,7 @@
                             <goal>format</goal>
                         </goals>
                         <configuration>
+                            <baseDir>${basedir}/src</baseDir>
                             <rewriteArrowSymbols>false</rewriteArrowSymbols>
                             <alignParameters>true</alignParameters>
                             <alignSingleLineCaseStatements_maxArrowIndent>40