diff --git a/docs/pipelines/flexiprep.md b/docs/pipelines/flexiprep.md
index cd1e3f8400e9b9bcce0e03fa8ee335e812bb562c..2140398ab88dd7ae89d99b23e9539b2a4dd4ad44 100644
--- a/docs/pipelines/flexiprep.md
+++ b/docs/pipelines/flexiprep.md
@@ -44,8 +44,8 @@ Command line flags for Flexiprep are:
| Flag (short)| Flag (long) | Type | Function |
| ------------ | ----------- | ---- | -------- |
-| -R1 | --input_r1 | Path (**required**) | Path to input fastq file |
-| -R2 | --input_r2 | Path (optional) | Path to second read pair fastq file. |
+| -R1 | --inputR1 | Path (**required**) | Path to input fastq file |
+| -R2 | --inputR2 | Path (optional) | Path to second read pair fastq file. |
| -sample | --sampleid | String (**required**) | Name of sample |
| -library | --libid | String (**required**) | Name of library |
diff --git a/docs/pipelines/mapping.md b/docs/pipelines/mapping.md
index f04efebc60425764eeb38cbeae90ca9f4751865b..79d2a57494ca3fb24e369515dcfed47b883bf556 100644
--- a/docs/pipelines/mapping.md
+++ b/docs/pipelines/mapping.md
@@ -28,8 +28,8 @@ Command line flags for the mapping pipeline are:
| Flag (short)| Flag (long) | Type | Function |
| ------------ | ----------- | ---- | -------- |
-| -R1 | --input_r1 | Path (**required**) | Path to input fastq file |
-| -R2 | --input_r2 | Path (optional) | Path to second read pair fastq file. |
+| -R1 | --inputR1 | Path (**required**) | Path to input fastq file |
+| -R2 | --inputR2 | Path (optional) | Path to second read pair fastq file. |
| -sample | --sampleid | String (**required**) | Name of sample |
| -library | --libid | String (**required**) | Name of library |
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala
index 9a4bbd07cd73ad59ed8cd36e4d15e1709f265578..2017d4c30da42cce13d4b10ac7ca3142e3f5f178 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala
@@ -265,8 +265,8 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
def summaryStats: Map[String, Any] = {
if (statsText) {
- val stats_file: File = new File(output.getAbsolutePath + "_summary.txt")
- parseStatsFile(stats_file)
+ val statsFile: File = new File(output.getAbsolutePath + "_summary.txt")
+ parseStatsFile(statsFile)
} else {
Map()
}
diff --git a/public/biopet-tools-extensions/src/test/scala/VcfFilterTest.scala b/public/biopet-tools-extensions/src/test/scala/VcfFilterTest.scala
index 8fddb1c78be5ddff4be3d948236afe94b164ab72..bb332f00e29dbbc098e3303c3167c6faf21ad45d 100644
--- a/public/biopet-tools-extensions/src/test/scala/VcfFilterTest.scala
+++ b/public/biopet-tools-extensions/src/test/scala/VcfFilterTest.scala
@@ -102,85 +102,45 @@ class VcfFilterTest extends TestNGSuite with Matchers {
val command = cmd(vcfFilter.cmdLine)
var cmdString: List[String] = Nil
- if (minSampleDepth.isDefined) {
- cmdString = "--minSampleDepth " + minSampleDepth.getOrElse("") :: cmdString
- }
+ if (minSampleDepth.isDefined) cmdString = "--minSampleDepth " + minSampleDepth.getOrElse("") :: cmdString
- if (minTotalDepth.isDefined) {
- cmdString = "--minTotalDepth " + minTotalDepth.getOrElse("") :: cmdString
- }
+ if (minTotalDepth.isDefined) cmdString = "--minTotalDepth " + minTotalDepth.getOrElse("") :: cmdString
- if (minAlternateDepth.isDefined) {
- cmdString = "--minAlternateDepth " + minAlternateDepth.getOrElse("") :: cmdString
- }
+ if (minAlternateDepth.isDefined) cmdString = "--minAlternateDepth " + minAlternateDepth.getOrElse("") :: cmdString
- if (minSamplesPass.isDefined) {
- cmdString = "--minSamplesPass " + minSamplesPass.getOrElse("") :: cmdString
- }
+ if (minSamplesPass.isDefined) cmdString = "--minSamplesPass " + minSamplesPass.getOrElse("") :: cmdString
- if (minGenomeQuality.isDefined) {
- cmdString = "--minGenomeQuality " + minGenomeQuality.getOrElse("") :: cmdString
- }
+ if (minGenomeQuality.isDefined) cmdString = "--minGenomeQuality " + minGenomeQuality.getOrElse("") :: cmdString
- if (filterRefCalls) {
- cmdString = "--filterRefCalls" :: cmdString
- }
+ if (filterRefCalls) cmdString = "--filterRefCalls" :: cmdString
- if (invertedOutputVcf.isDefined) {
- cmdString = "--invertedOutputVcf " + invertedOutputVcf.getOrElse(new File("")).getAbsolutePath :: cmdString
- }
+ if (invertedOutputVcf.isDefined) cmdString = "--invertedOutputVcf " + invertedOutputVcf.getOrElse(new File("")).getAbsolutePath :: cmdString
- if (resToDom.isDefined) {
- cmdString = "--resToDom " + resToDom.getOrElse("") :: cmdString
- }
+ if (resToDom.isDefined) cmdString = "--resToDom " + resToDom.getOrElse("") :: cmdString
- if (trioCompound.isDefined) {
- cmdString = "--trioCompound " + trioCompound.getOrElse("") :: cmdString
- }
+ if (trioCompound.isDefined) cmdString = "--trioCompound " + trioCompound.getOrElse("") :: cmdString
- if (deNovoInSample.isDefined) {
- cmdString = "--deNovoInSample " + deNovoInSample.getOrElse("") :: cmdString
- }
+ if (deNovoInSample.isDefined) cmdString = "--deNovoInSample " + deNovoInSample.getOrElse("") :: cmdString
- if (deNovoTrio.isDefined) {
- cmdString = "--deNovoTrio " + deNovoTrio.getOrElse("") :: cmdString
- }
+ if (deNovoTrio.isDefined) cmdString = "--deNovoTrio " + deNovoTrio.getOrElse("") :: cmdString
- if (trioLossOfHet.isDefined) {
- cmdString = "--trioLossOfHet " + trioLossOfHet.getOrElse("") :: cmdString
- }
+ if (trioLossOfHet.isDefined) cmdString = "--trioLossOfHet " + trioLossOfHet.getOrElse("") :: cmdString
- if (mustHaveVariant.nonEmpty) {
- cmdString = mustHaveVariant.map(x => "--mustHaveVariant " + x) ::: cmdString
- }
+ if (mustHaveVariant.nonEmpty) cmdString = mustHaveVariant.map(x => "--mustHaveVariant " + x) ::: cmdString
- if (calledIn.nonEmpty) {
- cmdString = calledIn.map(x => "--calledIn " + x) ::: cmdString
- }
+ if (calledIn.nonEmpty) cmdString = calledIn.map(x => "--calledIn " + x) ::: cmdString
- if (mustHaveGenotype.nonEmpty) {
- cmdString = mustHaveGenotype.map(x => "--mustHaveGenotype " + x) ::: cmdString
- }
+ if (mustHaveGenotype.nonEmpty) cmdString = mustHaveGenotype.map(x => "--mustHaveGenotype " + x) ::: cmdString
- if (diffGenotype.nonEmpty) {
- cmdString = diffGenotype.map(x => "--diffGenotype " + x) ::: cmdString
- }
+ if (diffGenotype.nonEmpty) cmdString = diffGenotype.map(x => "--diffGenotype " + x) ::: cmdString
- if (filterHetVarToHomVar.nonEmpty) {
- cmdString = filterHetVarToHomVar.map(x => "--filterHetVarToHomVar " + x) ::: cmdString
- }
+ if (filterHetVarToHomVar.nonEmpty) cmdString = filterHetVarToHomVar.map(x => "--filterHetVarToHomVar " + x) ::: cmdString
- if (id.nonEmpty) {
- cmdString = id.map(x => "--id " + x) ::: cmdString
- }
+ if (id.nonEmpty) cmdString = id.map(x => "--id " + x) ::: cmdString
- if (idFile.isDefined) {
- cmdString = "--idFile " + idFile.getOrElse(new File("")).getAbsolutePath :: cmdString
- }
+ if (idFile.isDefined) cmdString = "--idFile " + idFile.getOrElse(new File("")).getAbsolutePath :: cmdString
- if (minQualScore.isDefined) {
- cmdString = "--minQualScore " + minQualScore.getOrElse("") :: cmdString
- }
+ if (minQualScore.isDefined) cmdString = "--minQualScore " + minQualScore.getOrElse("") :: cmdString
cmdString.foreach(x => command.contains(x) shouldBe true)
}
diff --git a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/AnnotateVcfWithBedTest.scala b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/AnnotateVcfWithBedTest.scala
index 65af6ae0e36c062196fff6306321deac5028281b..0dfa028e21b2f4ce9c8d1af0b27915206f45d783 100644
--- a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/AnnotateVcfWithBedTest.scala
+++ b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/AnnotateVcfWithBedTest.scala
@@ -34,25 +34,25 @@ class AnnotateVcfWithBedTest extends TestNGSuite with MockitoSugar with Matchers
Paths.get(getClass.getResource(p).toURI).toString
}
- val vepped_path = resourcePath("/VEP_oneline.vcf")
+ val veppedPath = resourcePath("/VEP_oneline.vcf")
val bed = resourcePath("/rrna01.bed")
val rand = new Random()
@Test def testOutputTypeVcf() = {
val tmpPath = "/tmp/VcfFilter_" + rand.nextString(10) + ".vcf"
- val arguments: Array[String] = Array("-I", vepped_path, "-o", tmpPath, "-B", bed, "-f", "testing")
+ val arguments: Array[String] = Array("-I", veppedPath, "-o", tmpPath, "-B", bed, "-f", "testing")
main(arguments)
}
@Test def testOutputTypeBcf() = {
val tmpPath = "/tmp/VcfFilter_" + rand.nextString(10) + ".bcf"
- val arguments: Array[String] = Array("-I", vepped_path, "-o", tmpPath, "-B", bed, "-f", "testing")
+ val arguments: Array[String] = Array("-I", veppedPath, "-o", tmpPath, "-B", bed, "-f", "testing")
main(arguments)
}
@Test def testOutputTypeVcfGz() = {
val tmpPath = "/tmp/VcfFilter_" + rand.nextString(10) + ".vcf.gz"
- val arguments: Array[String] = Array("-I", vepped_path, "-o", tmpPath, "-B", bed, "-f", "testing")
+ val arguments: Array[String] = Array("-I", veppedPath, "-o", tmpPath, "-B", bed, "-f", "testing")
main(arguments)
}
diff --git a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/MergeAllelesTest.scala b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/MergeAllelesTest.scala
index 538948557f4a17c55d70d40c04c1ef4f384fd94e..d9c44abfc1ae29b8c1af7e453fc27d4a66cfc517 100644
--- a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/MergeAllelesTest.scala
+++ b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/MergeAllelesTest.scala
@@ -37,7 +37,7 @@ class MergeAllelesTest extends TestNGSuite with MockitoSugar with Matchers {
Paths.get(getClass.getResource(p).toURI).toString
}
- val vepped_path = resourcePath("/chrQ.vcf.gz")
+ val veppedPath = resourcePath("/chrQ.vcf.gz")
val reference = resourcePath("/fake_chrQ.fa")
// These two have to created
@@ -52,7 +52,7 @@ class MergeAllelesTest extends TestNGSuite with MockitoSugar with Matchers {
val tmp = File.createTempFile("MergeAlleles", ".vcf")
tmp.deleteOnExit()
val tmpPath = tmp.getAbsolutePath
- val arguments = Array("-I", vepped_path, "-o", tmpPath, "-R", reference)
+ val arguments = Array("-I", veppedPath, "-o", tmpPath, "-R", reference)
main(arguments)
}
@@ -60,7 +60,7 @@ class MergeAllelesTest extends TestNGSuite with MockitoSugar with Matchers {
val tmp = File.createTempFile("MergeAlleles", ".vcf.gz")
tmp.deleteOnExit()
val tmpPath = tmp.getAbsolutePath
- val arguments = Array("-I", vepped_path, "-o", tmpPath, "-R", reference)
+ val arguments = Array("-I", veppedPath, "-o", tmpPath, "-R", reference)
main(arguments)
}
@@ -68,7 +68,7 @@ class MergeAllelesTest extends TestNGSuite with MockitoSugar with Matchers {
val tmp = File.createTempFile("MergeAlleles", ".bcf")
tmp.deleteOnExit()
val tmpPath = tmp.getAbsolutePath
- val arguments = Array("-I", vepped_path, "-o", tmpPath, "-R", reference)
+ val arguments = Array("-I", veppedPath, "-o", tmpPath, "-R", reference)
main(arguments)
}
}
diff --git a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VcfFilterTest.scala b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VcfFilterTest.scala
index afe161575dfb1cfd9d01d360e7a49473aeadfdb4..50b342bc9509803fe03bb175d4c50b121b282297 100644
--- a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VcfFilterTest.scala
+++ b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VcfFilterTest.scala
@@ -39,31 +39,31 @@ class VcfFilterTest extends TestNGSuite with MockitoSugar with Matchers {
Paths.get(getClass.getResource(p).toURI).toString
}
- val vepped_path = resourcePath("/VEP_oneline.vcf")
- val vepped = new File(vepped_path)
+ val veppedPath = resourcePath("/VEP_oneline.vcf")
+ val vepped = new File(veppedPath)
val rand = new Random()
@Test def testOutputTypeVcf() = {
val tmp = File.createTempFile("VcfFilter", ".vcf")
tmp.deleteOnExit()
- val tmp_path = tmp.getAbsolutePath
- val arguments: Array[String] = Array("-I", vepped_path, "-o", tmp_path)
+ val tmpPath = tmp.getAbsolutePath
+ val arguments: Array[String] = Array("-I", veppedPath, "-o", tmpPath)
main(arguments)
}
@Test def testOutputTypeBcf() = {
val tmp = File.createTempFile("VcfFilter", ".bcf")
tmp.deleteOnExit()
- val tmp_path = tmp.getAbsolutePath
- val arguments: Array[String] = Array("-I", vepped_path, "-o", tmp_path)
+ val tmpPath = tmp.getAbsolutePath
+ val arguments: Array[String] = Array("-I", veppedPath, "-o", tmpPath)
main(arguments)
}
@Test def testOutputTypeVcfGz() = {
val tmp = File.createTempFile("VcfFilter", ".vcf.gz")
tmp.deleteOnExit()
- val tmp_path = tmp.getAbsolutePath
- val arguments: Array[String] = Array("-I", vepped_path, "-o", tmp_path)
+ val tmpPath = tmp.getAbsolutePath
+ val arguments: Array[String] = Array("-I", veppedPath, "-o", tmpPath)
main(arguments)
}
@@ -73,22 +73,22 @@ class VcfFilterTest extends TestNGSuite with MockitoSugar with Matchers {
*/
val tmp = File.createTempFile("VCfFilter", ".vcf.gz")
tmp.deleteOnExit()
- val tmp_path = tmp.getAbsolutePath
- val arguments: Array[String] = Array("-I", vepped_path, "-o", tmp_path,
+ val tmpPath = tmp.getAbsolutePath
+ val arguments: Array[String] = Array("-I", veppedPath, "-o", tmpPath,
"--mustHaveGenotype", "Sample_101:HET")
main(arguments)
- val size = new VCFFileReader(new File(tmp_path), false).size
+ val size = new VCFFileReader(new File(tmpPath), false).size
size shouldBe 1
val tmp2 = File.createTempFile("VcfFilter", ".vcf.gz")
tmp2.deleteOnExit()
- val tmp2_path = tmp2.getAbsolutePath
- val arguments2: Array[String] = Array("-I", vepped_path, "-o", tmp2_path,
+ val tmpPath2 = tmp2.getAbsolutePath
+ val arguments2: Array[String] = Array("-I", veppedPath, "-o", tmpPath2,
"--mustHaveGenotype", "Sample_101:HOM_VAR")
main(arguments2)
- val size2 = new VCFFileReader(new File(tmp2_path), false).size
+ val size2 = new VCFFileReader(new File(tmpPath2), false).size
size2 shouldBe 0
}
diff --git a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
index 5dd4dd9aaadd9da44bce94200f9ea49d594cbf69..ab87244ee6329c0163d91660df6e8f57f866949a 100644
--- a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
+++ b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
@@ -27,11 +27,11 @@ import org.broadinstitute.gatk.queue.QScript
class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with SampleLibraryTag {
def this() = this(null)
- @Input(doc = "R1 fastq file (gzipped allowed)", shortName = "R1", required = true)
+ @Input(doc = "R1 fastq file (gzipped allowed)", shortName = "R1", fullName = "inputR1", required = true)
var inputR1: File = _
- @Input(doc = "R2 fastq file (gzipped allowed)", shortName = "R2", required = false)
- var input_R2: Option[File] = None
+ @Input(doc = "R2 fastq file (gzipped allowed)", shortName = "R2", fullName = "inputR2", required = false)
+ var inputR2: Option[File] = None
/** Skip Trim fastq files */
var skipTrim: Boolean = config("skip_trim", default = false)
@@ -48,13 +48,13 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
/** Returns files to store in summary */
def summaryFiles: Map[String, File] = {
Map("input_R1" -> inputR1, "output_R1" -> fastqR1Qc) ++
- (if (paired) Map("input_R2" -> input_R2.get, "output_R2" -> fastqR2Qc.get) else Map())
+ (if (paired) Map("input_R2" -> inputR2.get, "output_R2" -> fastqR2Qc.get) else Map())
}
/** returns settings to store in summary */
def summarySettings = Map("skip_trim" -> skipTrim, "skip_clip" -> skipClip, "paired" -> paired)
- var paired: Boolean = input_R2.isDefined
+ var paired: Boolean = inputR2.isDefined
var R1Name: String = _
var R2Name: String = _
@@ -80,13 +80,13 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
require(sampleId != null, "Missing sample ID on flexiprep module")
require(libId != null, "Missing library ID on flexiprep module")
- paired = input_R2.isDefined
+ paired = inputR2.isDefined
inputFiles :+= new InputFile(inputR1)
- input_R2.foreach(inputFiles :+= new InputFile(_))
+ inputR2.foreach(inputFiles :+= new InputFile(_))
R1Name = getUncompressedFileName(inputR1)
- input_R2.foreach { fileR2 =>
+ inputR2.foreach { fileR2 =>
paired = true
R2Name = getUncompressedFileName(fileR2)
}
@@ -96,7 +96,7 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
def biopetScript() {
runInitialJobs()
- if (paired) runTrimClip(inputR1, input_R2, outputDir)
+ if (paired) runTrimClip(inputR1, inputR2, outputDir)
else runTrimClip(inputR1, outputDir)
val R1Files = for ((k, v) <- outputFiles if k.endsWith("output_R1")) yield v
@@ -107,7 +107,7 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
/** Add init non chunkable jobs */
def runInitialJobs() {
outputFiles += ("fastq_input_R1" -> inputR1)
- if (paired) outputFiles += ("fastq_input_R2" -> input_R2.get)
+ if (paired) outputFiles += ("fastq_input_R2" -> inputR2.get)
fastqcR1 = Fastqc(this, inputR1, new File(outputDir, R1Name + ".fastqc/"))
add(fastqcR1)
@@ -116,7 +116,7 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
val validateFastq = new ValidateFastq(this)
validateFastq.r1Fastq = inputR1
- validateFastq.r2Fastq = input_R2
+ validateFastq.r2Fastq = inputR2
validateFastq.jobOutputFile = new File(outputDir, ".validate_fastq.log.out")
add(validateFastq)
@@ -128,7 +128,7 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
}
if (paired) {
- fastqcR2 = Fastqc(this, input_R2.get, new File(outputDir, R2Name + ".fastqc/"))
+ fastqcR2 = Fastqc(this, inputR2.get, new File(outputDir, R2Name + ".fastqc/"))
add(fastqcR2)
addSummarizable(fastqcR2, "fastqc_R2")
outputFiles += ("fastqc_R2" -> fastqcR2.output)
@@ -140,7 +140,7 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
addSummarizable(seqstatR1, "seqstat_R1")
if (paired) {
- val seqstatR2 = SeqStat(this, input_R2.get, outputDir)
+ val seqstatR2 = SeqStat(this, inputR2.get, outputDir)
seqstatR2.isIntermediate = true
add(seqstatR2)
addSummarizable(seqstatR2, "seqstat_R2")
diff --git a/public/flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepTest.scala b/public/flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepTest.scala
index f4b6718944b7283d91d7ec06ec0f4317acdcc027..1f00c07a01e073d29e63c21e246d1c3c2dbc69d0 100644
--- a/public/flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepTest.scala
+++ b/public/flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepTest.scala
@@ -71,7 +71,7 @@ class FlexiprepTest extends TestNGSuite with Matchers {
val flexiprep: Flexiprep = initPipeline(map)
flexiprep.inputR1 = (if (zipped) FlexiprepTest.r1Zipped else FlexiprepTest.r1)
- if (paired) flexiprep.input_R2 = Some((if (zipped) FlexiprepTest.r2Zipped else FlexiprepTest.r2))
+ if (paired) flexiprep.inputR2 = Some((if (zipped) FlexiprepTest.r2Zipped else FlexiprepTest.r2))
flexiprep.sampleId = Some("1")
flexiprep.libId = Some("1")
flexiprep.script()
diff --git a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala b/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala
index d3c94062ca525dc6e80db4d5dd59edcb77de49a8..85902125b1900266dad66aaf2cf2fbbcfa6f467b 100644
--- a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala
+++ b/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala
@@ -98,7 +98,7 @@ class Gears(val root: Configurable) extends QScript with MultiSampleQScript { qs
flexiprep.sampleId = Some(sampleId)
flexiprep.libId = Some(libId)
flexiprep.inputR1 = config("R1")
- flexiprep.input_R2 = config("R2")
+ flexiprep.inputR2 = config("R2")
flexiprep.outputDir = new File(libDir, "flexiprep")
lazy val gs = new GearsSingle(qscript)
@@ -109,7 +109,7 @@ class Gears(val root: Configurable) extends QScript with MultiSampleQScript { qs
/** Function that add library jobs */
protected def addJobs(): Unit = {
inputFiles :+= InputFile(flexiprep.inputR1, config("R1_md5"))
- flexiprep.input_R2.foreach(inputFiles :+= InputFile(_, config("R2_md5")))
+ flexiprep.inputR2.foreach(inputFiles :+= InputFile(_, config("R2_md5")))
add(flexiprep)
gs.fastqR1 = Some(flexiprep.fastqR1Qc)
diff --git a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingle.scala b/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingle.scala
index 972307ed7bfd6522a6f2aeab627b640f10936a93..a01b088b47224078cc36f2f937715d10d3e5adf8 100644
--- a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingle.scala
+++ b/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingle.scala
@@ -80,7 +80,7 @@ class GearsSingle(val root: Configurable) extends QScript with SummaryQScript wi
if (!skipFlexiprep) {
val flexiprep = new Flexiprep(this)
flexiprep.inputR1 = r1
- flexiprep.input_R2 = r2
+ flexiprep.inputR2 = r2
flexiprep.outputDir = new File(outputDir, "flexiprep")
add(flexiprep)
(flexiprep.fastqR1Qc, flexiprep.fastqR2Qc)
diff --git a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/FragmentsPerGene.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/FragmentsPerGene.scala
index e6323699e4a488cf2c26b20ceb0ebeab3fbbf1b9..d1ae4398f0e8b4ad20acf3be0d5c3b694ddf6dad 100644
--- a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/FragmentsPerGene.scala
+++ b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/FragmentsPerGene.scala
@@ -9,7 +9,7 @@ import org.broadinstitute.gatk.queue.QScript
* Created by pjvan_thof on 1/12/16.
*/
class FragmentsPerGene(val root: Configurable) extends QScript with Measurement with AnnotationGtf {
- def mergeArgs = MergeArgs(List(1), 2, numHeaderLines = 1, fallback = "0")
+ def mergeArgs = MergeArgs(idCols = List(1), valCol = 2, numHeaderLines = 0, fallback = "0")
/** Pipeline itself */
def biopetScript(): Unit = {
diff --git a/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala b/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
index ed509aee9903f1a926101368f3bc82b908bacf67..fa1494e6c6693d28df1fea45c053a09dee52937d 100644
--- a/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
+++ b/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
@@ -41,10 +41,10 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
def this() = this(null)
- @Input(doc = "R1 fastq file", shortName = "R1", required = true)
+ @Input(doc = "R1 fastq file", shortName = "R1", fullName = "inputR1", required = true)
var inputR1: File = _
- @Input(doc = "R2 fastq file", shortName = "R2", required = false)
+ @Input(doc = "R2 fastq file", shortName = "R2", fullName = "inputR2", required = false)
var inputR2: Option[File] = None
/** Output name */
@@ -167,7 +167,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
if (!skipFlexiprep) {
flexiprep.outputDir = new File(outputDir, "flexiprep")
flexiprep.inputR1 = inputR1
- flexiprep.input_R2 = inputR2
+ flexiprep.inputR2 = inputR2
flexiprep.sampleId = this.sampleId
flexiprep.libId = this.libId
flexiprep.init()
@@ -184,7 +184,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
if (paired) Some(new File(chunkDir, inputR2.get.getName)) else None)
}).toMap
else if (skipFlexiprep) Map(outputDir -> (inputR1, if (paired) inputR2 else None))
- else Map(outputDir -> (flexiprep.inputR1, flexiprep.input_R2))
+ else Map(outputDir -> (flexiprep.inputR1, flexiprep.inputR2))
}
if (chunking) {