Commit dd937c3a authored by pjvan_thof's avatar pjvan_thof
Browse files

Merge remote-tracking branch 'remotes/origin/develop' into fix-BIOPET-718

parents 4989de28 9b83c7aa
...@@ -29,7 +29,7 @@ node('local') { ...@@ -29,7 +29,7 @@ node('local') {
sh 'mkdocs build --clean --strict' sh 'mkdocs build --clean --strict'
} }
if (currentBuild.result == null || "SUCCESS".equals(currentBuild.result)) { if (currentBuild.result == null || "SUCCESS" == currentBuild.result) {
currentBuild.result = "SUCCESS" currentBuild.result = "SUCCESS"
slackSend(color: '#00FF00', message: "${currentBuild.result}: Job '${env.JOB_NAME} #${env.BUILD_NUMBER}' (<${env.BUILD_URL}|Open>)", channel: '#biopet-bot', teamDomain: 'lumc', tokenCredentialId: 'lumc') slackSend(color: '#00FF00', message: "${currentBuild.result}: Job '${env.JOB_NAME} #${env.BUILD_NUMBER}' (<${env.BUILD_URL}|Open>)", channel: '#biopet-bot', teamDomain: 'lumc', tokenCredentialId: 'lumc')
} else { } else {
...@@ -37,7 +37,7 @@ node('local') { ...@@ -37,7 +37,7 @@ node('local') {
} }
} catch (e) { } catch (e) {
if (currentBuild.result == null || "FAILED".equals(currentBuild.result)) { if (currentBuild.result == null || "FAILED" == currentBuild.result) {
currentBuild.result = "FAILED" currentBuild.result = "FAILED"
} }
slackSend(color: '#FF0000', message: "${currentBuild.result}: Job '${env.JOB_NAME} #${env.BUILD_NUMBER}' (<${env.BUILD_URL}|Open>)", channel: '#biopet-bot', teamDomain: 'lumc', tokenCredentialId: 'lumc') slackSend(color: '#FF0000', message: "${currentBuild.result}: Job '${env.JOB_NAME} #${env.BUILD_NUMBER}' (<${env.BUILD_URL}|Open>)", channel: '#biopet-bot', teamDomain: 'lumc', tokenCredentialId: 'lumc')
......
...@@ -31,7 +31,7 @@ class Bam2Wig(val parent: Configurable) extends QScript with BiopetQScript { ...@@ -31,7 +31,7 @@ class Bam2Wig(val parent: Configurable) extends QScript with BiopetQScript {
def this() = this(null) def this() = this(null)
@Input(doc = "Input bam file", required = true) @Input(doc = "Input bam file", required = true)
var bamFile: File = null var bamFile: File = _
def init(): Unit = { def init(): Unit = {
inputFiles :+= new InputFile(bamFile) inputFiles :+= new InputFile(bamFile)
......
...@@ -32,7 +32,7 @@ class BamToChromSizesTest extends TestNGSuite with Matchers { ...@@ -32,7 +32,7 @@ class BamToChromSizesTest extends TestNGSuite with Matchers {
} }
@Test @Test
def testChromSizes: Unit = { def testChromSizes(): Unit = {
val bamFile = new File(resourcePath("/empty.bam")) val bamFile = new File(resourcePath("/empty.bam"))
val bamToChromSizes = new BamToChromSizes(null) val bamToChromSizes = new BamToChromSizes(null)
bamToChromSizes.bamFile = bamFile bamToChromSizes.bamFile = bamFile
......
...@@ -13,8 +13,8 @@ ...@@ -13,8 +13,8 @@
<tr><th>Version</th><td>${run.version}</td></tr> <tr><th>Version</th><td>${run.version}</td></tr>
<tr><th>Last commit hash</th><td>${run.commitHash}</td></tr> <tr><th>Last commit hash</th><td>${run.commitHash}</td></tr>
<tr><th>Output directory</th><td>${run.outputDir}</td></tr> <tr><th>Output directory</th><td>${run.outputDir}</td></tr>
<tr><th>Sample</th><td>${allSamples.filter(_.id == sampleId.get).headOption.map(_.name)}</td></tr> <tr><th>Sample</th><td>${allSamples.find(_.id == sampleId.get).map(_.name)}</td></tr>
<tr><th>Library</th><td>${allLibraries.filter(_.id == libId.get).headOption.map(_.name)}</td></tr> <tr><th>Library</th><td>${allLibraries.find(_.id == libId.get).map(_.name)}</td></tr>
</tbody> </tbody>
</table> </table>
<br/> <br/>
......
...@@ -48,7 +48,7 @@ class BamMetrics(val parent: Configurable) ...@@ -48,7 +48,7 @@ class BamMetrics(val parent: Configurable)
override def defaults = Map("bedtoolscoverage" -> Map("sorted" -> true)) override def defaults = Map("bedtoolscoverage" -> Map("sorted" -> true))
/** returns files to store in summary */ /** returns files to store in summary */
def summaryFiles = def summaryFiles: Map[String, File] =
Map("reference" -> referenceFasta(), "input_bam" -> inputBam) ++ Map("reference" -> referenceFasta(), "input_bam" -> inputBam) ++
ampliconBedFile.map("amplicon" -> _).toMap ++ ampliconBedFile.map("amplicon" -> _).toMap ++
ampliconBedFile.map(x => "roi_" + x.getName.stripSuffix(".bed") -> x).toMap ampliconBedFile.map(x => "roi_" + x.getName.stripSuffix(".bed") -> x).toMap
...@@ -58,7 +58,7 @@ class BamMetrics(val parent: Configurable) ...@@ -58,7 +58,7 @@ class BamMetrics(val parent: Configurable)
Map("amplicon_name" -> ampliconBedFile.collect { case x => x.getName.stripSuffix(".bed") }, Map("amplicon_name" -> ampliconBedFile.collect { case x => x.getName.stripSuffix(".bed") },
"roi_name" -> roiBedFiles.map(_.getName.stripSuffix(".bed"))) "roi_name" -> roiBedFiles.map(_.getName.stripSuffix(".bed")))
override def reportClass = { override def reportClass: Some[BammetricsReport] = {
val bammetricsReport = new BammetricsReport(this) val bammetricsReport = new BammetricsReport(this)
bammetricsReport.outputDir = new File(outputDir, "report") bammetricsReport.outputDir = new File(outputDir, "report")
bammetricsReport.summaryDbFile = summaryDbFile bammetricsReport.summaryDbFile = summaryDbFile
......
...@@ -487,7 +487,7 @@ object BammetricsReport extends ReportBuilder { ...@@ -487,7 +487,7 @@ object BammetricsReport extends ReportBuilder {
} }
def writeTableToTsv(tsvFile: File, table: Map[String, Array[Any]], firstColumn: String): Unit = { def writeTableToTsv(tsvFile: File, table: Map[String, Array[Any]], firstColumn: String): Unit = {
require(table.map(_._2.size).toList.distinct.size == 1, require(table.map(_._2.length).toList.distinct.size == 1,
"Not all values has the same number or rows") "Not all values has the same number or rows")
val keys = table.keys.filterNot(_ == firstColumn).toList.sorted val keys = table.keys.filterNot(_ == firstColumn).toList.sorted
val writer = new PrintWriter(tsvFile) val writer = new PrintWriter(tsvFile)
......
...@@ -44,7 +44,7 @@ class BamMetricsTest extends TestNGSuite with Matchers { ...@@ -44,7 +44,7 @@ class BamMetricsTest extends TestNGSuite with Matchers {
} }
@DataProvider(name = "bammetricsOptions") @DataProvider(name = "bammetricsOptions")
def bammetricsOptions = { def bammetricsOptions: Array[Array[AnyVal]] = {
val rois = Array(0, 1, 2, 3) val rois = Array(0, 1, 2, 3)
val bool = Array(true, false) val bool = Array(true, false)
...@@ -57,7 +57,7 @@ class BamMetricsTest extends TestNGSuite with Matchers { ...@@ -57,7 +57,7 @@ class BamMetricsTest extends TestNGSuite with Matchers {
private var dirs: List[File] = Nil private var dirs: List[File] = Nil
@Test(dataProvider = "bammetricsOptions") @Test(dataProvider = "bammetricsOptions")
def testBamMetrics(rois: Int, amplicon: Boolean, rna: Boolean, wgs: Boolean) = { def testBamMetrics(rois: Int, amplicon: Boolean, rna: Boolean, wgs: Boolean): Unit = {
val outputDir = Files.createTempDir() val outputDir = Files.createTempDir()
dirs :+= outputDir dirs :+= outputDir
val map = ConfigUtils.mergeMaps(Map("output_dir" -> outputDir, val map = ConfigUtils.mergeMaps(Map("output_dir" -> outputDir,
...@@ -74,8 +74,6 @@ class BamMetricsTest extends TestNGSuite with Matchers { ...@@ -74,8 +74,6 @@ class BamMetricsTest extends TestNGSuite with Matchers {
bammetrics.libId = Some("1") bammetrics.libId = Some("1")
bammetrics.script() bammetrics.script()
var regions: Int = rois + (if (amplicon) 1 else 0)
bammetrics.functions.count(_.isInstanceOf[CollectRnaSeqMetrics]) shouldBe (if (rna) 1 else 0) bammetrics.functions.count(_.isInstanceOf[CollectRnaSeqMetrics]) shouldBe (if (rna) 1 else 0)
bammetrics.functions.count(_.isInstanceOf[CollectWgsMetrics]) shouldBe (if (wgs) 1 else 0) bammetrics.functions.count(_.isInstanceOf[CollectWgsMetrics]) shouldBe (if (wgs) 1 else 0)
bammetrics.functions.count(_.isInstanceOf[CollectMultipleMetrics]) shouldBe 1 bammetrics.functions.count(_.isInstanceOf[CollectMultipleMetrics]) shouldBe 1
...@@ -86,13 +84,13 @@ class BamMetricsTest extends TestNGSuite with Matchers { ...@@ -86,13 +84,13 @@ class BamMetricsTest extends TestNGSuite with Matchers {
} }
// remove temporary run directory all tests in the class have been run // remove temporary run directory all tests in the class have been run
@AfterClass def removeTempOutputDir() = { @AfterClass def removeTempOutputDir(): Unit = {
dirs.foreach(FileUtils.deleteDirectory) dirs.foreach(FileUtils.deleteDirectory)
} }
} }
object BamMetricsTest { object BamMetricsTest {
val inputDir = Files.createTempDir() val inputDir: File = Files.createTempDir()
val bam = new File(inputDir, "bla.bam") val bam = new File(inputDir, "bla.bam")
Files.touch(bam) Files.touch(bam)
...@@ -100,7 +98,7 @@ object BamMetricsTest { ...@@ -100,7 +98,7 @@ object BamMetricsTest {
Files.touch(ampliconBed) Files.touch(ampliconBed)
def roi(i: Int): File = { def roi(i: Int): File = {
val roi = new File(inputDir, s"roi${i}.bed") val roi = new File(inputDir, s"roi$i.bed")
Files.touch(roi) Files.touch(roi)
roi roi
} }
......
...@@ -42,7 +42,7 @@ class Basty(val parent: Configurable) extends QScript with MultiSampleQScript { ...@@ -42,7 +42,7 @@ class Basty(val parent: Configurable) extends QScript with MultiSampleQScript {
def variantcallers = List("unifiedgenotyper") def variantcallers = List("unifiedgenotyper")
val numBoot = config("boot_runs", default = 100, namespace = "raxml").asInt val numBoot: Int = config("boot_runs", default = 100, namespace = "raxml").asInt
override def defaults = Map( override def defaults = Map(
"ploidy" -> 1, "ploidy" -> 1,
......
...@@ -48,7 +48,7 @@ class BastyTest extends TestNGSuite with Matchers { ...@@ -48,7 +48,7 @@ class BastyTest extends TestNGSuite with Matchers {
} }
@DataProvider(name = "bastyOptions") @DataProvider(name = "bastyOptions")
def bastyOptions = { def bastyOptions: Array[Array[Any]] = {
for (s1 <- sample1; s2 <- sample2) yield Array("", s1, s2) for (s1 <- sample1; s2 <- sample2) yield Array("", s1, s2)
} }
...@@ -114,7 +114,7 @@ class BastyTest extends TestNGSuite with Matchers { ...@@ -114,7 +114,7 @@ class BastyTest extends TestNGSuite with Matchers {
numberSamples numberSamples
else 0) else 0)
pipeline.functions.count(_.isInstanceOf[BaseRecalibrator]) shouldBe (if (dbsnp && baseRecalibration) pipeline.functions.count(_.isInstanceOf[BaseRecalibrator]) shouldBe (if (dbsnp && baseRecalibration)
(numberLibs * 2) numberLibs * 2
else 0) else 0)
pipeline.functions.count(_.isInstanceOf[PrintReads]) shouldBe (if (dbsnp && baseRecalibration) pipeline.functions.count(_.isInstanceOf[PrintReads]) shouldBe (if (dbsnp && baseRecalibration)
numberLibs numberLibs
...@@ -125,7 +125,7 @@ class BastyTest extends TestNGSuite with Matchers { ...@@ -125,7 +125,7 @@ class BastyTest extends TestNGSuite with Matchers {
pipeline.summaryFiles shouldBe Map() pipeline.summaryFiles shouldBe Map()
pipeline.samples foreach { pipeline.samples foreach {
case (sampleId, sample) => case (_, sample) =>
sample.summarySettings shouldBe Map() sample.summarySettings shouldBe Map()
sample.summaryFiles.get("variants_fasta") should not be None sample.summaryFiles.get("variants_fasta") should not be None
sample.summaryFiles.get("consensus_fasta") should not be None sample.summaryFiles.get("consensus_fasta") should not be None
...@@ -135,7 +135,7 @@ class BastyTest extends TestNGSuite with Matchers { ...@@ -135,7 +135,7 @@ class BastyTest extends TestNGSuite with Matchers {
sample.summaryFiles.get("snps_only_consensus_variants_fasta") should not be None sample.summaryFiles.get("snps_only_consensus_variants_fasta") should not be None
sample.summaryStats shouldBe Map() sample.summaryStats shouldBe Map()
sample.libraries.foreach { sample.libraries.foreach {
case (libId, lib) => case (_, lib) =>
lib.summarySettings shouldBe Map() lib.summarySettings shouldBe Map()
lib.summaryFiles shouldBe Map() lib.summaryFiles shouldBe Map()
lib.summaryStats shouldBe Map() lib.summaryStats shouldBe Map()
...@@ -154,14 +154,14 @@ class BastyTest extends TestNGSuite with Matchers { ...@@ -154,14 +154,14 @@ class BastyTest extends TestNGSuite with Matchers {
} }
// remove temporary run directory all tests in the class have been run // remove temporary run directory all tests in the class have been run
@AfterClass def removeTempOutputDir() = { @AfterClass def removeTempOutputDir(): Unit = {
dirs.foreach(FileUtils.deleteDirectory) dirs.foreach(FileUtils.deleteDirectory)
} }
} }
object BastyTest { object BastyTest {
def outputDir = Files.createTempDir() def outputDir: File = Files.createTempDir()
val inputDir = Files.createTempDir() val inputDir: File = Files.createTempDir()
def inputTouch(name: String): String = { def inputTouch(name: String): String = {
val file = new File(inputDir, name) val file = new File(inputDir, name)
......
...@@ -150,10 +150,9 @@ body { ...@@ -150,10 +150,9 @@ body {
float:right; float:right;
width:0; width:0;
height:0; height:0;
border-color:transparent; border: 5px solid transparent;
border-style:solid; border-right-width: 0;
border-width:5px 0 5px 5px; border-left-color: #cccccc;
border-left-color:#cccccc;
margin-top:5px; margin-top:5px;
margin-right:-10px; margin-right:-10px;
} }
......
...@@ -46,9 +46,7 @@ table[data-sortable] th:after { ...@@ -46,9 +46,7 @@ table[data-sortable] th:after {
vertical-align: inherit; vertical-align: inherit;
height: 0; height: 0;
width: 0; width: 0;
border-width: 5px; border: 5px solid transparent;
border-style: solid;
border-color: transparent;
margin-right: 1px; margin-right: 1px;
margin-left: 10px; margin-left: 10px;
float: right; float: right;
......
...@@ -31,9 +31,9 @@ ...@@ -31,9 +31,9 @@
<tbody> <tbody>
#for (file <- files) #for (file <- files)
<tr><td>${allPipelines.find(_.id == file.pipelineId).map(_.name)}</td> <tr><td>${allPipelines.find(_.id == file.pipelineId).map(_.name)}</td>
<td>${file.moduleId.map(id => allModules.find(x => x.pipelineId == file.pipelineId && file.moduleId == id).map(_.name)).flatten.getOrElse(("-"))}</td> <td>${file.moduleId.flatMap(id => allModules.find(x => x.pipelineId == file.pipelineId && file.moduleId == id).map(_.name)).getOrElse("-")}</td>
<td>${file.sampleId.map(id => allSamples.find(_.id == id).map(_.name)).flatten.getOrElse(("-"))}</td> <td>${file.sampleId.flatMap(id => allSamples.find(_.id == id).map(_.name)).getOrElse("-")}</td>
<td>${file.libraryId.map(id => allLibraries.find(_.id == id).map(_.name)).flatten.getOrElse(("-"))}</td> <td>${file.libraryId.flatMap(id => allLibraries.find(_.id == id).map(_.name)).getOrElse("-")}</td>
<td>${file.key}</td> <td>${file.key}</td>
<td>${file.path}</td> <td>${file.path}</td>
<td>${file.md5}</td></tr> <td>${file.md5}</td></tr>
......
...@@ -42,7 +42,7 @@ ...@@ -42,7 +42,7 @@
val tabIndex = if (first) " tabindex='-1'" else "" val tabIndex = if (first) " tabindex='-1'" else ""
// val listGroupA = if(subPage._2.subPages.nonEmpty) "list-group-item" else "" // val listGroupA = if(subPage._2.subPages.nonEmpty) "list-group-item" else ""
var menuItem: String = "<li class='%s'>".format(listSubmenu) + val menuItem: String = "<li class='%s'>".format(listSubmenu) +
"<a href='%s' class='%s'%s>".format(href, "", tabIndex) + "<a href='%s' class='%s'%s>".format(href, "", tabIndex) +
"%s".format(subPageName) + "%s".format(subPageName) +
"</a>" + "</a>" +
...@@ -93,7 +93,7 @@ ...@@ -93,7 +93,7 @@
<script language="JavaScript"> <script language="JavaScript">
<!-- <!--
$(document).ready(function() { $(document).ready(function() {
Sortable.init() Sortable.init();
$('body').scrollspy({ $('body').scrollspy({
target: '.bs-sidebar' target: '.bs-sidebar'
...@@ -135,14 +135,14 @@ ...@@ -135,14 +135,14 @@
<a href="${rootPath}index.html">Home <a href="${rootPath}index.html">Home
#if (iPage.subPages.nonEmpty) <b class="caret"></b> #end #if (iPage.subPages.nonEmpty) <b class="caret"></b> #end
</a> </a>
${unescape(createMenu(iPage, Nil, false))} ${unescape(createMenu(iPage, Nil, first = false))}
</li> </li>
#else #else
<li class="root #if (t == path.size) active #end"> <li class="root #if (t == path.size) active #end">
<a href="${rootPath}${path.slice(0,t).mkString("", "/", "/")}index.html">${path( t - 1 )} <a href="${rootPath}${path.slice(0,t).mkString("", "/", "/")}index.html">${path( t - 1 )}
#if (getSubPage(path.slice(0, t)).subPages.nonEmpty) <b class="caret"></b> #end #if (getSubPage(path.slice(0, t)).subPages.nonEmpty) <b class="caret"></b> #end
</a> </a>
${unescape(createMenu(getSubPage(path.slice(0, t)), path.slice(0, t), false))} ${unescape(createMenu(getSubPage(path.slice(0, t)), path.slice(0, t), first = false))}
</li> </li>
#end #end
#end #end
......
...@@ -60,10 +60,10 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction => ...@@ -60,10 +60,10 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
} }
/** /**
* This value is used to let you job wait a x number of second after it finish. * This value is used to let you job wait a x number of second after it finish.
* This is ionly used when having storage delay issues * This is ionly used when having storage delay issues
*/ */
var jobDelayTime: Option[Int] = config("job_delay_time") val jobDelayTime: Option[Int] = config("job_delay_time")
// This overrides the default "sh" from queue. For Biopet the default is "bash" // This overrides the default "sh" from queue. For Biopet the default is "bash"
updateJobRun = { updateJobRun = {
...@@ -147,9 +147,9 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction => ...@@ -147,9 +147,9 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
} }
private[core] var _inputAsStdin = false private[core] var _inputAsStdin = false
def inputAsStdin = _inputAsStdin def inputAsStdin: Boolean = _inputAsStdin
private[core] var _outputAsStdout = false private[core] var _outputAsStdout = false
def outputAsStdout = _outputAsStdout def outputAsStdout: Boolean = _outputAsStdout
/** /**
* This operator sends stdout to `that` and combine this into 1 command line function * This operator sends stdout to `that` and combine this into 1 command line function
...@@ -212,13 +212,13 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction => ...@@ -212,13 +212,13 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
maxGroups: Int = 0): String = { maxGroups: Int = 0): String = {
if (values.size % groupSize != 0) if (values.size % groupSize != 0)
Logging.addError( Logging.addError(
s"Arg '${argName}' values: '${values}' does not fit to a groupSize of ${groupSize}") s"Arg '$argName' values: '$values' does not fit to a groupSize of $groupSize")
val groups = values.size / groupSize val groups = values.size / groupSize
if (groups < minGroups) if (groups < minGroups)
Logging.addError(s"Args '${argName}' need atleast $minGroups with size $groupSize") Logging.addError(s"Args '$argName' need atleast $minGroups with size $groupSize")
if (maxGroups > 0 && groups > maxGroups) if (maxGroups > 0 && groups > maxGroups)
Logging.addError(s"Args '${argName}' may only have $maxGroups with size $groupSize") Logging.addError(s"Args '$argName' may only have $maxGroups with size $groupSize")
if (values.nonEmpty) required(argName) + values.map(required(_)).mkString if (values.nonEmpty) required(argName) + values.map(required).mkString
else "" else ""
} }
...@@ -251,7 +251,7 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction => ...@@ -251,7 +251,7 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
} }
private[core] var _pipesJobs: List[BiopetCommandLineFunction] = Nil private[core] var _pipesJobs: List[BiopetCommandLineFunction] = Nil
def pipesJobs = _pipesJobs def pipesJobs: List[BiopetCommandLineFunction] = _pipesJobs
def addPipeJob(job: BiopetCommandLineFunction) { def addPipeJob(job: BiopetCommandLineFunction) {
_pipesJobs :+= job _pipesJobs :+= job
_pipesJobs = _pipesJobs.distinct _pipesJobs = _pipesJobs.distinct
......
...@@ -30,7 +30,7 @@ trait BiopetJavaCommandLineFunction ...@@ -30,7 +30,7 @@ trait BiopetJavaCommandLineFunction
override def defaultVmemFactor: Double = 2.0 override def defaultVmemFactor: Double = 2.0
/** Constructs java opts, this adds scala threads */ /** Constructs java opts, this adds scala threads */
override def javaOpts = override def javaOpts: String =
super.javaOpts + super.javaOpts +
optional("-Dscala.concurrent.context.numThreads=", threads, spaceSeparated = false) + optional("-Dscala.concurrent.context.numThreads=", threads, spaceSeparated = false) +
optional("-Dscala.concurrent.context.maxThreads=", threads, spaceSeparated = false) optional("-Dscala.concurrent.context.maxThreads=", threads, spaceSeparated = false)
......
...@@ -30,14 +30,14 @@ class BiopetPipe(val commands: List[BiopetCommandLineFunction]) extends BiopetCo ...@@ -30,14 +30,14 @@ class BiopetPipe(val commands: List[BiopetCommandLineFunction]) extends BiopetCo
lazy val input: List[File] = try { lazy val input: List[File] = try {
commands.flatMap(_.inputs) commands.flatMap(_.inputs)
} catch { } catch {
case e: Exception => Nil case _: Exception => Nil
} }
@Output @Output
lazy val output: List[File] = try { lazy val output: List[File] = try {
commands.flatMap(_.outputs) commands.flatMap(_.outputs)
} catch { } catch {
case e: Exception => Nil case _: Exception => Nil
} }
_pipesJobs :::= commands _pipesJobs :::= commands
...@@ -74,7 +74,7 @@ class BiopetPipe(val commands: List[BiopetCommandLineFunction]) extends BiopetCo ...@@ -74,7 +74,7 @@ class BiopetPipe(val commands: List[BiopetCommandLineFunction]) extends BiopetCo
override def defaultThreads = 0 override def defaultThreads = 0
val parent: Configurable = commands.head.parent val parent: Configurable = commands.head.parent
override def configNamespace = commands.map(_.configNamespace).mkString("-") override def configNamespace: String = commands.map(_.configNamespace).mkString("-")
def cmdLine: String = { def cmdLine: String = {
"(" + commands.head.cmdLine + (if (commands.head.stdinFile.isDefined) { "(" + commands.head.cmdLine + (if (commands.head.stdinFile.isDefined) {
" < " + required( " < " + required(
...@@ -90,4 +90,4 @@ class BiopetPipe(val commands: List[BiopetCommandLineFunction]) extends BiopetCo ...@@ -90,4 +90,4 @@ class BiopetPipe(val commands: List[BiopetCommandLineFunction]) extends BiopetCo
super.freezeFieldValues() super.freezeFieldValues()
commands.foreach(_.qSettings = qSettings) commands.foreach(_.qSettings = qSettings)
} }
} }
\ No newline at end of file
...@@ -221,7 +221,7 @@ object BiopetQScript { ...@@ -221,7 +221,7 @@ object BiopetQScript {
try { try {
Some(function.inputs) Some(function.inputs)
} catch { } catch {
case e: NullPointerException => None case _: NullPointerException => None
} }
} }
...@@ -229,7 +229,7 @@ object BiopetQScript { ...@@ -229,7 +229,7 @@ object BiopetQScript {
try { try {
Some(function.outputs) Some(function.outputs)
} catch { } catch {
case e: NullPointerException => None case _: NullPointerException => None
} }
}