diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
index 2f098dfaa24c9d1bc31ab0c2d1f4f09c7124f10f..44a7e780f3d50839916a67fe152b1df4d9ce448a 100644
--- a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
@@ -18,7 +18,8 @@ package nl.lumc.sasc.biopet.core
import java.io.{ File, FileInputStream }
import java.security.MessageDigest
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.Logging
+import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.function.CommandLineFunction
import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
@@ -110,7 +111,7 @@ trait BiopetCommandLineFunction extends CommandLineFunction with Configurable {
if (executableToCanonicalPath) executable = file.getCanonicalPath
else executable = file.getAbsolutePath
} else {
- BiopetQScript.addError("executable: '" + executable + "' not found, please check config")
+ Logging.addError("executable: '" + executable + "' not found, please check config")
}
BiopetCommandLineFunction.executableCache += oldExecutable -> executable
BiopetCommandLineFunction.executableCache += executable -> executable
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetPipe.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetPipe.scala
similarity index 93%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetPipe.scala
rename to public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetPipe.scala
index 8cd0737ac21bddc84cd407f3cd16338d30bfd667..40b546bde641419bf3d4bad17595268bee9f3cb1 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetPipe.scala
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetPipe.scala
@@ -2,8 +2,8 @@ package nl.lumc.sasc.biopet.core
import java.io.File
-import nl.lumc.sasc.biopet.core.config.Configurable
-import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/**
* This class can pipe multiple BiopetCommandFunctions to 1 job
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/core/BiopetPipeTest.scala b/public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/BiopetPipeTest.scala
similarity index 100%
rename from public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/core/BiopetPipeTest.scala
rename to public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/BiopetPipeTest.scala
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BastyGenerateFasta.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BastyGenerateFasta.scala
index 9b0020ae21e8626f3f987aaec2d1bd2921374bed..bc1d672269421ce7be6d64d15d0f8841c81332a1 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BastyGenerateFasta.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BastyGenerateFasta.scala
@@ -55,7 +55,7 @@ class BastyGenerateFasta(val root: Configurable) extends ToolCommandFuntion with
reference = referenceFasta()
}
- override def commandLine = super.commandLine +
+ override def cmdLine = super.cmdLine +
optional("--inputVcf", inputVcf) +
optional("--bamFile", bamFile) +
optional("--outputVariants", outputVariants) +
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BedToInterval.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BedToInterval.scala
index bab2f7c0ae0fa260a78ff366d9e9f4a6c177d9f6..f7f00d0f94d43dcc45724c3ed4b61715072b88c1 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BedToInterval.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BedToInterval.scala
@@ -38,7 +38,7 @@ class BedToInterval(val root: Configurable) extends ToolCommandFuntion {
override def defaultCoreMemory = 1.0
- override def commandLine = super.commandLine + required("-I", input) + required("-b", bamFile) + required("-o", output)
+ override def cmdLine = super.cmdLine + required("-I", input) + required("-b", bamFile) + required("-o", output)
}
object BedToInterval {
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BedtoolsCoverageToCounts.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BedtoolsCoverageToCounts.scala
index 817b6d3f2792168a8f4fdf8549fa3c16c858e21e..00a77a5e9d9ac4ec1e5c2d02ed350cdf53b10d5d 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BedtoolsCoverageToCounts.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BedtoolsCoverageToCounts.scala
@@ -32,7 +32,7 @@ class BedtoolsCoverageToCounts(val root: Configurable) extends ToolCommandFuntio
override def defaultCoreMemory = 3.0
- override def commandLine = super.commandLine +
+ override def cmdLine = super.cmdLine +
required("-I", input) +
required("-o", output)
}
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BiopetFlagstat.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BiopetFlagstat.scala
index ff06bc963764f07563aa4ca0e2926119ba667c9b..5dc69cb07a34f04ed2cc32e7069875649c3aa32b 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BiopetFlagstat.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BiopetFlagstat.scala
@@ -37,7 +37,7 @@ class BiopetFlagstat(val root: Configurable) extends ToolCommandFuntion with Sum
override def defaultCoreMemory = 6.0
- override def commandLine = super.commandLine + required("-I", input) + required("-s", summaryFile) + " > " + required(output)
+ override def cmdLine = super.cmdLine + required("-I", input) + required("-s", summaryFile) + " > " + required(output)
def summaryFiles: Map[String, File] = Map()
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/FastqSplitter.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/FastqSplitter.scala
index df7e32e19bacfc8021ec015fcf019f9f16f61fe2..7348048447ca6c614b3b43ba915b228e042e9a37 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/FastqSplitter.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/FastqSplitter.scala
@@ -37,7 +37,7 @@ class FastqSplitter(val root: Configurable) extends ToolCommandFuntion {
override def defaultCoreMemory = 4.0
/** * Generate command to execute */
- override def commandLine = super.commandLine +
+ override def cmdLine = super.cmdLine +
required("-I", input) +
repeat("-o", output)
}
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/FastqSync.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/FastqSync.scala
index 90100c8e7942afe8dd105ca64ba2ff5990747b7f..4d56c8e4912f086f232f030eca98cf37113be157 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/FastqSync.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/FastqSync.scala
@@ -55,8 +55,8 @@ class FastqSync(val root: Configurable) extends ToolCommandFuntion with Summariz
override def defaultCoreMemory = 4.0
// executed command line
- override def commandLine =
- super.commandLine +
+ override def cmdLine =
+ super.cmdLine +
required("-r", refFastq) +
required("-i", inputFastq1) +
required("-j", inputFastq2) +
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MergeAlleles.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MergeAlleles.scala
index eedb51fdd1bb9d07d405299cb9dbf913681fbb96..504c7cb7c830cf8d1fa067b9048e7f23f4e3fe06 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MergeAlleles.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MergeAlleles.scala
@@ -43,7 +43,7 @@ class MergeAlleles(val root: Configurable) extends ToolCommandFuntion {
if (output.getName.endsWith(".vcf")) outputIndex = new File(output.getAbsolutePath + ".idx")
}
- override def commandLine = super.commandLine +
+ override def cmdLine = super.cmdLine +
repeat("-I", input) +
required("-o", output) +
required("-R", reference)
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MergeTables.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MergeTables.scala
index 96a421db3e706d0220df76b6acfd5aab9cda9480..15ca55b6a524b283418ad67476d41b384541beb7 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MergeTables.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MergeTables.scala
@@ -65,8 +65,8 @@ class MergeTables(val root: Configurable) extends ToolCommandFuntion {
var delimiter: Option[String] = config("delimiter")
// executed command line
- override def commandLine =
- super.commandLine +
+ override def cmdLine =
+ super.cmdLine +
required("-i", idColumnIndices.mkString(",")) +
required("-a", valueColumnIndex) +
optional("-n", idColumnName) +
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MpileupToVcf.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MpileupToVcf.scala
index 5a3e1e3f26588c103a4bf5e0a190aa223d064450..212641116f93c61ea9ef1412c7228297cdbb4ff6 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MpileupToVcf.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MpileupToVcf.scala
@@ -66,14 +66,14 @@ class MpileupToVcf(val root: Configurable) extends ToolCommandFuntion with Refer
}
}
- override def commandLine = {
+ override def cmdLine = {
(if (inputMpileup == null) {
val samtoolsMpileup = new SamtoolsMpileup(this)
samtoolsMpileup.reference = referenceFasta()
samtoolsMpileup.input = List(inputBam)
samtoolsMpileup.cmdPipe + " | "
} else "") +
- super.commandLine +
+ super.cmdLine +
required("-o", output) +
optional("--minDP", minDP) +
optional("--minAP", minAP) +
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/PrefixFastq.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/PrefixFastq.scala
index 302aa11586119a6602f29b0b452ed0645aeb2c37..dca36baf399c3f90725f61843ead5ed4416a08ab 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/PrefixFastq.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/PrefixFastq.scala
@@ -44,7 +44,7 @@ class PrefixFastq(val root: Configurable) extends ToolCommandFuntion {
* Creates command to execute extension
* @return
*/
- override def commandLine = super.commandLine +
+ override def cmdLine = super.cmdLine +
required("-i", inputFastq) +
required("-o", outputFastq) +
optional("-s", prefixSeq)
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCountFastq.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCountFastq.scala
index 2ee9d97e17ef35cbf6573bf0fa91bb5fc8f76b2c..0e71324dba7091729f044ff6b0815c04d5c937dd 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCountFastq.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCountFastq.scala
@@ -32,7 +32,7 @@ class SageCountFastq(val root: Configurable) extends ToolCommandFuntion {
override def defaultCoreMemory = 3.0
- override def commandLine = super.commandLine +
+ override def cmdLine = super.cmdLine +
required("-I", input) +
required("-o", output)
}
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCreateLibrary.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCreateLibrary.scala
index 4b287d2cefaf98c777ca2ad44084f74bfacf5047..a2d79430f008d0a5818d98ae6ded6258ab74be0a 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCreateLibrary.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCreateLibrary.scala
@@ -44,7 +44,7 @@ class SageCreateLibrary(val root: Configurable) extends ToolCommandFuntion {
override def defaultCoreMemory = 3.0
- override def commandLine = super.commandLine +
+ override def cmdLine = super.cmdLine +
required("-I", input) +
optional("--tag", tag) +
optional("--length", length) +
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCreateTagCounts.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCreateTagCounts.scala
index d0779973b4484f29264bc574af6d898e1df8804d..30e7f524f65000789653085e4c6443a4e8a6d4a8 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCreateTagCounts.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCreateTagCounts.scala
@@ -44,7 +44,7 @@ class SageCreateTagCounts(val root: Configurable) extends ToolCommandFuntion {
override def defaultCoreMemory = 3.0
- override def commandLine = super.commandLine +
+ override def cmdLine = super.cmdLine +
required("-I", input) +
required("--tagLib", tagLib) +
optional("--countSense", countSense) +
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SeqStat.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SeqStat.scala
index cc7a8e6ede5bb1ba0d318639e8b9320a0ae8024a..3f1cf95a447f3f13827a27b82073fbf98e628495 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SeqStat.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SeqStat.scala
@@ -24,7 +24,7 @@ class SeqStat(val root: Configurable) extends ToolCommandFuntion with Summarizab
override def defaultCoreMemory = 2.5
- override def commandLine = super.commandLine + required("-i", input) + required("-o", output)
+ override def cmdLine = super.cmdLine + required("-i", input) + required("-o", output)
def summaryStats: Map[String, Any] = {
val map = ConfigUtils.fileToConfigMap(output)
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SquishBed.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SquishBed.scala
index 558c93f8532b95ccd3dfa33e3265f0fbebda8104..f42f635be866d88fd92c9991c93f93afb9e880cd 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SquishBed.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SquishBed.scala
@@ -20,7 +20,7 @@ class SquishBed(val root: Configurable) extends ToolCommandFuntion {
var strandSensitive: Boolean = config("strandSensitive", default = false)
- override def commandLine = super.commandLine +
+ override def cmdLine = super.cmdLine +
required("-I", input) +
required("-o", output) +
conditional(strandSensitive, "-s")
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfFilter.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfFilter.scala
index 60d550532dfd30150e63f11096237356aa182a1a..06af56f025692658ad19c4e8375e7b81fbe599fc 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfFilter.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfFilter.scala
@@ -38,7 +38,7 @@ class VcfFilter(val root: Configurable) extends ToolCommandFuntion {
override def defaultCoreMemory = 3.0
- override def commandLine = super.commandLine +
+ override def cmdLine = super.cmdLine +
required("-I", inputVcf) +
required("-o", outputVcf) +
optional("--minSampleDepth", minSampleDepth) +
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfStats.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfStats.scala
index 3fd09a67fb74b3759ec3f00c51344f88afc53231..d0024681b727e6f72fdc31da7483bb7b1c98b4f6 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfStats.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfStats.scala
@@ -69,7 +69,7 @@ class VcfStats(val root: Configurable) extends ToolCommandFuntion with Summariza
}
/** Creates command to execute extension */
- override def commandLine = super.commandLine +
+ override def cmdLine = super.cmdLine +
required("-I", input) +
required("-o", outputDir) +
repeat("--infoTag", infoTags) +
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfWithVcf.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfWithVcf.scala
index 5ab877502eaef6133b51a1927c83b94dc5b7b3ba..e956f5c93f5de3d9243de7bb5c9c1684de8f3fa4 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfWithVcf.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfWithVcf.scala
@@ -50,7 +50,7 @@ class VcfWithVcf(val root: Configurable) extends ToolCommandFuntion {
if (fields.isEmpty) throw new IllegalArgumentException("No fields found for VcfWithVcf")
}
- override def commandLine = super.commandLine +
+ override def cmdLine = super.cmdLine +
required("-I", input) +
required("-o", output) +
required("-s", secondaryVcf) +
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VepNormalizer.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VepNormalizer.scala
index 4379b990dd585b012b15a44a7fc0605a7772b898..229f39628c9d1f8f8e23400b96a4fea957028e71 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VepNormalizer.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VepNormalizer.scala
@@ -45,7 +45,7 @@ class VepNormalizer(val root: Configurable) extends ToolCommandFuntion {
override def defaultCoreMemory = 4.0
- override def commandLine = super.commandLine +
+ override def cmdLine = super.cmdLine +
required("-I", inputVCF) +
required("-O", outputVcf) +
required("-m", mode) +