Merge branch 'develop' into BIOWDL-78

.gitignore

 *.jar
+target/

build.sbt

+organization := "com.github.biopet"
+organizationName := "Biowdl"
+name := "tasks"
+
+biopetUrlName := "tasks"
+
+startYear := Some(2018)
+
+biopetIsTool := false
+biopetIsPipeline := true
+
+developers += Developer(id = "DavyCats",
+                        name = "Davy Cats",
+                        email = "d.cats@lumc.nl",
+                        url = url("https://github.com/DavyCats"))
+developers += Developer(id = "rhpvorderman",
+                        name = "Ruben Vorderman",
+                        email = "r.h.p.vorderman@lumc.nl",
+                        url = url("https://github.com/rhpvorderman"))
+
+scalaVersion := "2.11.12"
+
+libraryDependencies += "com.github.biopet" %% "biowdl-test-utils" % "0.2-SNAPSHOT" % Test changing ()

multiqc.wdl

+version 1.0
+
+task MultiQC {
+    input {
+        String? preCommand
+        File analysisDirectory
+        Array[File] dependencies   # This must be used in order to run multiqc after these tasks.
+        Boolean force = false
+        Boolean dirs = false
+        Int? dirsDepth
+        Boolean fullNames = false
+        String? title
+        String? comment
+        String? fileName
+        String outDir = "."
+        String? template
+        String? tag
+        String? ignore
+        String? ignoreSamples
+        Boolean ignoreSymlinks = false
+        File? sampleNames
+        File? fileList
+        Array[String]+? exclude
+        Array[String]+? module
+        Boolean dataDir = false
+        Boolean noDataDir = false
+        String? dataFormat
+        Boolean zipDataDir = false
+        Boolean export = false
+        Boolean flat = false
+        Boolean interactive = false
+        Boolean lint = false
+        Boolean pdf = false
+        Boolean megaQCUpload = false # This must be actively enabled in my opinion. The tools default is to upload.
+        File? config  # A directory
+        String? clConfig
+        Boolean verbose  = false
+        Boolean quiet = false
+    }
+
+    command {
+        set -e -o pipefail
+        ~{preCommand}
+        mkdir -p ~{outDir}
+        multiqc \
+        ~{true="--force" false="" force} \
+        ~{true="--dirs" false="" dirs} \
+        ~{"--dirs-depth " + dirsDepth} \
+        ~{true="--fullnames" false="" fullNames} \
+        ~{"--title " + title} \
+        ~{"--comment " + comment} \
+        ~{"--filename " + fileName} \
+        ~{"--outdir " + outDir} \
+        ~{"--template " + template} \
+        ~{"--tag " + tag} \
+        ~{"--ignore " + ignore} \
+        ~{"--ignore-samples" + ignoreSamples} \
+        ~{true="--ignore-symlinks" false="" ignoreSymlinks} \
+        ~{"--sample-names " + sampleNames} \
+        ~{"--file-list " + fileList} \
+        ~{true="--exclude " false="" defined(exclude)}~{sep=" --exclude " exclude} \
+        ~{true="--module " false="" defined(module)}~{sep=" --module " module} \
+        ~{true="--data-dir" false="" dataDir} \
+        ~{true="--no-data-dir" false="" noDataDir} \
+        ~{"--data-format " + dataFormat} \
+        ~{true="--zip-data-dir" false="" zipDataDir} \
+        ~{true="--export" false="" export} \
+        ~{true="--flat" false="" flat} \
+        ~{true="--interactive" false="" interactive} \
+        ~{true="--lint" false="" lint} \
+        ~{true="--pdf" false="" pdf} \
+        ~{false="--no-megaqc-upload" true="" megaQCUpload} \
+        ~{"--config " + config} \
+        ~{"--cl-config " + clConfig } \
+        ~{analysisDirectory}
+    }
+
+    String reportFilename = if (defined(fileName)) then sub(select_first([fileName]), "\.html$", "") else "multiqc"
+    output {
+        File multiqcReport = outDir + "/" + reportFilename + "_report.html"
+        File multiqcDataDir = outDir + "/" +reportFilename + "_data"
+    }
+}

project/build.properties

+sbt.version=1.0.4

project/plugins.sbt

+addSbtPlugin("com.github.biopet" % "sbt-biopet" % "0.9.0")

version.sbt

+version in ThisBuild := "0.2-SNAPSHOT"