diff --git a/docs/developer/getting-started.md b/docs/developer/getting-started.md
index 744237ac0f9e77ba9c1d6477cd49a0a60775d169..83768ebea63f1227274e30d353aa7fd04b2644b4 100644
--- a/docs/developer/getting-started.md
+++ b/docs/developer/getting-started.md
@@ -4,14 +4,22 @@
- Maven 3.3
- Installed Gatk to maven local repository (see below)
- Installed Biopet to maven local repository (see below)
+- Some knowledge of the programming language [Scala](http://www.scala-lang.org/) (The pipelines are scripted using Scala)
+- We encourage users to use an IDE for scripting the pipeline. One that works pretty well for us is: [IntelliJ IDEA](https://www.jetbrains.com/idea/)
+
+To start the development of a biopet pipeline you should have the following tools installed:
+
+* Gatk
+* Biopet
+
+Make sure both tools are installed in your local maven repository. To do this one should use the commands below.
-To start to develop a biopet pipeline you should have installed Gatk and Biopet in your local maven repository. Do to this execute the follow command.
```bash
-# Replace 'mvn' for to location of you maven executable or make put it in your PATH
+# Replace 'mvn' with the location of you maven executable or put it in your PATH with the export command.
git clone https://github.com/broadgsa/gatk-protected
cd gatk-protected
git checkout 3.4
-# This version is bound to a version of Biopet, Biopet 0.5.0 using Gatk 3.4
+# The GATK version is bound to a version of Biopet. Biopet 0.5.0 uses Gatk 3.4
mvn clean install
cd ..
@@ -20,7 +28,6 @@ git clone https://github.com/biopet/biopet.git
cd biopet
git checkout 0.5.0
mvn -DskipTests=true clean install
-
```
### Basic components
@@ -28,7 +35,155 @@ mvn -DskipTests=true clean install
#### Qscript (pipeline)
A basic pipeline would look like this.
+```scala
+package org.example.group.pipelines
+
+import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import nl.lumc.sasc.biopet.extensions.{ Gzip, Cat }
+import org.broadinstitute.gatk.queue.QScript
+
+//TODO: Replace class name, must be the same as the class of the pipeline
+class SimplePipeline(val root: Configurable) extends QScript with BiopetQScript {
+ // A constructor without arguments is needed if this pipeline is a root pipeline
+ def this() = this(null)
+
+ @Input(required = true)
+ var inputFile: File = null
+
+ /** This method can be used to initialize some classes where needed */
+ def init(): Unit = {
+ }
+
+ /** This method is the actual pipeline */
+ def biopetScript: Unit = {
+ val cat = new Cat(this)
+ cat.input :+= inputFile
+ cat.output = new File(outputDir, "file.out")
+ add(cat)
+
+ val gzip = new Gzip(this)
+ gzip.input :+= cat.output
+ gzip.output = new File(outputDir, "file.out.gz")
+ add(gzip)
+ }
+}
+
+//TODO: Replace object name, must be the same as the class of the pipeline
+object SimplePipeline extends PipelineCommand
+```
+
#### Extensions (wrappers)
+Wrappers have to be written for each tool used inside the pipeline. A basic wrapper (example wraps the linux ```cat``` command) would look like this:
+```scala
+package nl.lumc.sasc.biopet.extensions
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+
+/**
+ * Extension for GNU cat
+ */
+class Cat(val root: Configurable) extends BiopetCommandLineFunction {
+ @Input(doc = "Input file", required = true)
+ var input: List[File] = Nil
+
+ @Output(doc = "Unzipped file", required = true)
+ var output: File = _
+
+ executable = config("exe", default = "cat")
+
+ /** return commandline to execute */
+ def cmdLine = required(executable) + repeat(input) + " > " + required(output)
+}
+```
+
+#### Tools (Scala programs)
+Within the Biopet framework it is also possible to write your own tools in Scala. If a give functionality or script is not incorporated within the framework
+one can write a tool that does the job. Below you can see an example tool which is written for automatically building sample configs.
+
+```scala
+package nl.lumc.sasc.biopet.tools
+
+import java.io.{ PrintWriter, File }
+
+import nl.lumc.sasc.biopet.utils.ConfigUtils._
+import nl.lumc.sasc.biopet.utils.ToolCommand
+import scala.collection.mutable
+
+import scala.io.Source
+
+/**
+ * This tool can convert a tsv to a json file
+ */
+object SamplesTsvToJson extends ToolCommand {
+ case class Args(inputFiles: List[File] = Nil, outputFile: Option[File] = None) extends AbstractArgs
+
+ class OptParser extends AbstractOptParser {
+ opt[File]('i', "inputFiles") required () unbounded () valueName "<file>" action { (x, c) =>
+ c.copy(inputFiles = x :: c.inputFiles)
+ } text "Input must be a tsv file, first line is seen as header and must at least have a 'sample' column, 'library' column is optional, multiple files allowed"
+ opt[File]('o', "outputFile") unbounded () valueName "<file>" action { (x, c) =>
+ c.copy(outputFile = Some(x))
+ }
+ }
+
+ /** Executes SamplesTsvToJson */
+ def main(args: Array[String]): Unit = {
+ val argsParser = new OptParser
+ val commandArgs: Args = argsParser.parse(args, Args()) getOrElse sys.exit(1)
+
+ val jsonString = stringFromInputs(commandArgs.inputFiles)
+ commandArgs.outputFile match {
+ case Some(file) => {
+ val writer = new PrintWriter(file)
+ writer.println(jsonString)
+ writer.close()
+ }
+ case _ => println(jsonString)
+ }
+ }
+
+ def mapFromFile(inputFile: File): Map[String, Any] = {
+ val reader = Source.fromFile(inputFile)
+ val lines = reader.getLines().toList.filter(!_.isEmpty)
+ val header = lines.head.split("\t")
+ val sampleColumn = header.indexOf("sample")
+ val libraryColumn = header.indexOf("library")
+ if (sampleColumn == -1) throw new IllegalStateException("Sample column does not exist in: " + inputFile)
+
+ val sampleLibCache: mutable.Set[(String, Option[String])] = mutable.Set()
+
+ val librariesValues: List[Map[String, Any]] = for (tsvLine <- lines.tail) yield {
+ val values = tsvLine.split("\t")
+ require(header.length == values.length, "Number of columns is not the same as the header")
+ val sample = values(sampleColumn)
+ val library = if (libraryColumn != -1) Some(values(libraryColumn)) else None
+
+ //FIXME: this is a workaround, should be removed after fixing #180
+ if (sample.head.isDigit || library.forall(_.head.isDigit))
+ throw new IllegalStateException("Sample or library may not start with a number")
+ if (sampleLibCache.contains((sample, library)))
+ throw new IllegalStateException(s"Combination of $sample ${library.map("and " + _).getOrElse("")} is found multiple times")
+ else sampleLibCache.add((sample, library))
+ val valuesMap = (for (
+ t <- 0 until values.size if !values(t).isEmpty && t != sampleColumn && t != libraryColumn
+ ) yield header(t) -> values(t)).toMap
+ library match {
+ case Some(lib) => Map("samples" -> Map(sample -> Map("libraries" -> Map(lib -> valuesMap))))
+ case _ => Map("samples" -> Map(sample -> valuesMap))
+ }
+ }
+ librariesValues.foldLeft(Map[String, Any]())((acc, kv) => mergeMaps(acc, kv))
+ }
-#### Tools (scala programs)
\ No newline at end of file
+ def stringFromInputs(inputs: List[File]): String = {
+ val map = inputs.map(f => mapFromFile(f)).foldLeft(Map[String, Any]())((acc, kv) => mergeMaps(acc, kv))
+ mapToJson(map).spaces2
+ }
+}
+```
\ No newline at end of file