diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala
new file mode 100644
index 0000000000000000000000000000000000000000..660c3b271100b6aace1ae6af01464ce18d60d74a
--- /dev/null
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala
@@ -0,0 +1,45 @@
+package nl.lumc.sasc.biopet.extensions
+
+
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+
+import java.io.File
+import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
+import nl.lumc.sasc.biopet.core.config.Configurable
+
+class Cutadapt(val root: Configurable) extends BiopetCommandLineFunction {
+ @Input(doc = "Input fastq file")
+ var fastq_input: File = _
+
+ @Output(doc = "Output fastq file")
+ var fastq_output: File = _
+
+ @Output(doc = "Output statistics file")
+ var stats_output: File = _
+
+ executable = config("exe", default = "cutadapt")
+ override def versionCommand = executable + " --version"
+ override val versionRegex = """(.*)""".r
+
+ var default_clip_mode: String = config("default_clip_mode", default = "3")
+ var opt_adapter: Set[String] = Set() + config("adapter")
+ var opt_anywhere: Set[String] = Set() + config("anywhere")
+ var opt_front: Set[String] = Set() + config("front")
+
+ var opt_discard: Boolean = config("discard")
+ var opt_minimum_length: String = config("minimum_length", 1)
+ var opt_maximum_length: String = config("maximum_length")
+
+ def cmdLine = required(executable) +
+ // options
+ repeat("-a", opt_adapter) +
+ repeat("-b", opt_anywhere) +
+ repeat("-g", opt_front) +
+ conditional(opt_discard, "--discard") +
+ optional("-m", opt_minimum_length) +
+ optional("-M", opt_maximum_length) +
+ // input / output
+ required(fastq_input) +
+ required("--output", fastq_output) +
+ " > " + required(stats_output)
+}
\ No newline at end of file
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
new file mode 100644
index 0000000000000000000000000000000000000000..2755877a632641b9fe3a2a70f097aefb99d0a78e
--- /dev/null
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
@@ -0,0 +1,52 @@
+package nl.lumc.sasc.biopet.extensions
+
+import java.io.File
+
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+
+import nl.lumc.sasc.biopet.core._
+import nl.lumc.sasc.biopet.core.config._
+
+class Fastqc(val root: Configurable) extends BiopetCommandLineFunction {
+
+ @Input(doc = "Contaminants", required = false)
+ var contaminants: File = _
+
+ @Input(doc = "Fastq file", shortName = "FQ")
+ var fastqfile: File = _
+
+ @Output(doc = "Output", shortName = "out")
+ var output: File = _
+
+ executable = config("exe", default = "fastqc")
+ var java_exe: String = config("exe", default = "java", submodule = "java")
+ var kmers: Option[Int] = config("kmers")
+ var quiet: Boolean = config("quiet")
+ var noextract: Boolean = config("noextract")
+ var nogroup: Boolean = config("nogroup")
+ var extract: Boolean = config("extract", default = true)
+
+ override val versionRegex = """FastQC (.*)""".r
+ override def versionCommand = executable + " --version"
+ override val defaultThreads = 4
+
+ override def afterGraph {
+ this.checkExecutable
+ if (contaminants == null) {
+ val fastqcDir = executable.substring(0, executable.lastIndexOf("/"))
+ contaminants = new File(fastqcDir + "/Contaminants/contaminant_list.txt")
+ }
+ }
+
+ def cmdLine = required(executable) +
+ optional("--java", java_exe) +
+ optional("--threads", threads) +
+ optional("--contaminants", contaminants) +
+ optional("--kmers", kmers) +
+ conditional(nogroup, "--nogroup") +
+ conditional(noextract, "--noextract") +
+ conditional(extract, "--extract") +
+ conditional(quiet, "--quiet") +
+ required("-o", output.getParent()) +
+ required(fastqfile)
+}
diff --git a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/extensions/fastq/Sickle.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala
similarity index 61%
rename from flexiprep/src/main/scala/nl/lumc/sasc/biopet/extensions/fastq/Sickle.scala
rename to biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala
index 7adb96bea25c13c61bfe878f519eb1094decad7d..1f4e0f9d4a5b576c61f71a00d9dd7fc193332ff1 100644
--- a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/extensions/fastq/Sickle.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala
@@ -1,16 +1,10 @@
-package nl.lumc.sasc.biopet.extensions.fastq
+package nl.lumc.sasc.biopet.extensions
import java.io.File
-import scala.io.Source._
-import scala.sys.process._
-import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
-
-import argonaut._, Argonaut._
-import scalaz._, Scalaz._
-
-import nl.lumc.sasc.biopet.core._
-import nl.lumc.sasc.biopet.core.config._
+import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
+import nl.lumc.sasc.biopet.core.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
class Sickle(val root: Configurable) extends BiopetCommandLineFunction {
@Input(doc = "R1 input")
@@ -19,9 +13,6 @@ class Sickle(val root: Configurable) extends BiopetCommandLineFunction {
@Input(doc = "R2 input", required = false)
var input_R2: File = _
- @Input(doc = "qualityType file", required = false)
- var qualityTypeFile: File = _
-
@Output(doc = "R1 output")
var output_R1: File = _
@@ -41,17 +32,12 @@ class Sickle(val root: Configurable) extends BiopetCommandLineFunction {
var defaultQualityType: String = config("defaultqualitytype", default = "sanger")
override val versionRegex = """sickle version (.*)""".r
+ override def versionCommand = executable + " --version"
override def afterGraph {
if (qualityType == null && defaultQualityType != null) qualityType = defaultQualityType
}
- override def versionCommand = executable + " --version"
-
- override def beforeCmd {
- qualityType = getQualityTypeFromFile
- }
-
def cmdLine = {
var cmd: String = required(executable)
if (input_R2 != null) {
@@ -67,26 +53,4 @@ class Sickle(val root: Configurable) extends BiopetCommandLineFunction {
required("-o", output_R1) +
" > " + required(output_stats)
}
-
- def getQualityTypeFromFile: String = {
- if (qualityType == null && qualityTypeFile != null) {
- if (qualityTypeFile.exists()) {
- for (line <- fromFile(qualityTypeFile).getLines) {
- var s: String = line.substring(0, line.lastIndexOf("\t"))
- return s
- }
- } else logger.warn("File : " + qualityTypeFile + " does not exist")
- }
- return null
- }
-
- def getSummary: Json = {
- return jNull
- }
}
-
-object Sickle {
- def mergeSummarys(jsons: List[Json]): Json = {
- return jNull
- }
-}
\ No newline at end of file
diff --git a/flexiprep/nbactions.xml b/flexiprep/nbactions.xml
index 47a3066de0a03bad99551b797774d36eec6c34e0..03bcc3800f70aa075482399d3d093ec4aa219019 100644
--- a/flexiprep/nbactions.xml
+++ b/flexiprep/nbactions.xml
@@ -10,7 +10,7 @@
<goal>org.codehaus.mojo:exec-maven-plugin:1.2.1:exec</goal>
</goals>
<properties>
- <exec.args>-classpath %classpath nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep -R2 bla.fastq.gz -R1 ../input_R1.fastq.bz2 -outputDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/flexiprep/examples/test.json -l DEBUG</exec.args>
+ <exec.args>-classpath %classpath nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep -R2 bla.fastq.gz -R1 ../input_R1.fastq.bz2 -outDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/flexiprep/examples/test.json -l DEBUG</exec.args>
<exec.executable>java</exec.executable>
<exec.workingdir>/home/pjvan_thof/pipelines/test</exec.workingdir>
</properties>
@@ -25,7 +25,7 @@
<goal>org.codehaus.mojo:exec-maven-plugin:1.2.1:exec</goal>
</goals>
<properties>
- <exec.args>-Xdebug -Xrunjdwp:transport=dt_socket,server=n,address=${jpda.address} -classpath %classpath nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep -R2 bla.fastq.gz -R1 ../input_R1.fastq.bz2 -outputDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/flexiprep/examples/test.json -l DEBUG</exec.args>
+ <exec.args>-Xdebug -Xrunjdwp:transport=dt_socket,server=n,address=${jpda.address} -classpath %classpath nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep -R2 bla.fastq.gz -R1 ../input_R1.fastq.bz2 -outDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/flexiprep/examples/test.json -l DEBUG</exec.args>
<exec.executable>java</exec.executable>
<jpda.listen>true</jpda.listen>
<exec.workingdir>/home/pjvan_thof/pipelines/test</exec.workingdir>
@@ -41,7 +41,7 @@
<goal>org.codehaus.mojo:exec-maven-plugin:1.2.1:exec</goal>
</goals>
<properties>
- <exec.args>-classpath %classpath nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep -R2 bla.fastq.gz -R1 ../input_R1.fastq.bz2 -outputDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/flexiprep/examples/test.json -l DEBUG</exec.args>
+ <exec.args>-classpath %classpath nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep -R2 bla.fastq.gz -R1 ../input_R1.fastq.bz2 -outDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/flexiprep/examples/test.json -l DEBUG</exec.args>
<exec.executable>java</exec.executable>
<exec.workingdir>/home/pjvan_thof/pipelines/test</exec.workingdir>
</properties>
diff --git a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/extensions/fastq/Cutadapt.scala b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/extensions/fastq/Cutadapt.scala
deleted file mode 100644
index 5b3baaaffe1f18591c41a681aa29e1aa4e8257f2..0000000000000000000000000000000000000000
--- a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/extensions/fastq/Cutadapt.scala
+++ /dev/null
@@ -1,98 +0,0 @@
-package nl.lumc.sasc.biopet.extensions.fastq
-
-import java.io.File
-import scala.io.Source._
-import scala.sys.process._
-
-import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
-
-import argonaut._, Argonaut._
-import scalaz._, Scalaz._
-
-import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
-import nl.lumc.sasc.biopet.core.config.Configurable
-import nl.lumc.sasc.biopet.extensions.Ln
-
-class Cutadapt(val root: Configurable) extends BiopetCommandLineFunction {
- @Input(doc = "Input fastq file")
- var fastq_input: File = _
-
- @Input(doc = "Fastq contams file", required = false)
- var contams_file: File = _
-
- @Output(doc = "Output fastq file")
- var fastq_output: File = _
-
- @Output(doc = "Output statistics file")
- var stats_output: File = _
-
- executable = config("exe", default = "cutadapt")
- override def versionCommand = executable + " --version"
- override val versionRegex = """(.*)""".r
-
- var default_clip_mode: String = config("default_clip_mode", default = "3")
- var opt_adapter: Set[String] = Set() + config("adapter")
- var opt_anywhere: Set[String] = Set() + config("anywhere")
- var opt_front: Set[String] = Set() + config("front")
-
- var opt_discard: Boolean = config("discard")
- var opt_minimum_length: String = config("minimum_length", 1)
- var opt_maximum_length: String = config("maximum_length")
-
- override def beforeCmd() {
- getContamsFromFile
- }
-
- def cmdLine = {
- if (!opt_adapter.isEmpty || !opt_anywhere.isEmpty || !opt_front.isEmpty) {
- analysisName = getClass.getName
- required(executable) +
- // options
- repeat("-a", opt_adapter) +
- repeat("-b", opt_anywhere) +
- repeat("-g", opt_front) +
- conditional(opt_discard, "--discard") +
- optional("-m", opt_minimum_length) +
- optional("-M", opt_maximum_length) +
- // input / output
- required(fastq_input) +
- required("--output", fastq_output) +
- " > " + required(stats_output)
- } else {
- analysisName = getClass.getSimpleName + "-ln"
- val lnOut = new Ln(this)
- lnOut.in = new java.io.File(required(fastq_input))
- lnOut.out = new java.io.File(required(fastq_output))
- lnOut.relative = true
- lnOut.cmd
- }
- }
-
- def getContamsFromFile {
- if (contams_file != null) {
- if (contams_file.exists()) {
- for (line <- fromFile(contams_file).getLines) {
- var s: String = line.substring(line.lastIndexOf("\t") + 1, line.size)
- if (default_clip_mode == "3") opt_adapter += s
- else if (default_clip_mode == "5") opt_front += s
- else if (default_clip_mode == "both") opt_anywhere += s
- else {
- opt_adapter += s
- logger.warn("Option default_clip_mode should be '3', '5' or 'both', falling back to default: '3'")
- }
- logger.info("Adapter: " + s + " found in: " + fastq_input)
- }
- } else logger.warn("File : " + contams_file + " does not exist")
- }
- }
-
- def getSummary: Json = {
- return jNull
- }
-}
-
-object Cutadapt {
- def mergeSummarys(jsons: List[Json]): Json = {
- return jNull
- }
-}
diff --git a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Cutadapt.scala b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Cutadapt.scala
new file mode 100644
index 0000000000000000000000000000000000000000..6de5da34f8eb40d049f8756034791441ead6f092
--- /dev/null
+++ b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Cutadapt.scala
@@ -0,0 +1,70 @@
+/*
+ * To change this license header, choose License Headers in Project Properties.
+ * To change this template file, choose Tools | Templates
+ * and open the template in the editor.
+ */
+
+package nl.lumc.sasc.biopet.pipelines.flexiprep
+
+import scala.io.Source
+
+import nl.lumc.sasc.biopet.extensions.Ln
+import org.broadinstitute.gatk.utils.commandline.{ Input }
+
+import argonaut._, Argonaut._
+import scalaz._, Scalaz._
+
+import java.io.File
+import nl.lumc.sasc.biopet.core.config.Configurable
+
+class Cutadapt(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Cutadapt(root) {
+ @Input(doc = "Fastq contams file", required = false)
+ var contams_file: File = _
+
+ override def beforeCmd() {
+ super.beforeCmd
+ getContamsFromFile
+ }
+
+ override def cmdLine = {
+ if (!opt_adapter.isEmpty || !opt_anywhere.isEmpty || !opt_front.isEmpty) {
+ analysisName = getClass.getName
+ super.cmdLine
+ } else {
+ analysisName = getClass.getSimpleName + "-ln"
+ val lnOut = new Ln(this)
+ lnOut.in = new java.io.File(required(fastq_input))
+ lnOut.out = new java.io.File(required(fastq_output))
+ lnOut.relative = true
+ lnOut.cmd
+ }
+ }
+
+ def getContamsFromFile {
+ if (contams_file != null) {
+ if (contams_file.exists()) {
+ for (line <- Source.fromFile(contams_file).getLines) {
+ var s: String = line.substring(line.lastIndexOf("\t") + 1, line.size)
+ if (default_clip_mode == "3") opt_adapter += s
+ else if (default_clip_mode == "5") opt_front += s
+ else if (default_clip_mode == "both") opt_anywhere += s
+ else {
+ opt_adapter += s
+ logger.warn("Option default_clip_mode should be '3', '5' or 'both', falling back to default: '3'")
+ }
+ logger.info("Adapter: " + s + " found in: " + fastq_input)
+ }
+ } else logger.warn("File : " + contams_file + " does not exist")
+ }
+ }
+
+ def getSummary: Json = {
+ return jNull
+ }
+}
+
+object Cutadapt {
+ def mergeSummarys(jsons: List[Json]): Json = {
+ return jNull
+ }
+}
diff --git a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/extensions/fastq/Fastqc.scala b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala
similarity index 50%
rename from flexiprep/src/main/scala/nl/lumc/sasc/biopet/extensions/fastq/Fastqc.scala
rename to flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala
index 3d9dcb2e3c804d9cedc29c790eb585dc750c4e94..b8ef6b7a545f31e0cf9cb46fa63ee7e52d91b3a5 100644
--- a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/extensions/fastq/Fastqc.scala
+++ b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala
@@ -1,63 +1,19 @@
-package nl.lumc.sasc.biopet.extensions.fastq
+/*
+ * To change this license header, choose License Headers in Project Properties.
+ * To change this template file, choose Tools | Templates
+ * and open the template in the editor.
+ */
+
+package nl.lumc.sasc.biopet.pipelines.flexiprep
import java.io.File
+import nl.lumc.sasc.biopet.core.config.Configurable
import scala.io.Source
-import scala.sys.process._
-
-import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import argonaut._, Argonaut._
import scalaz._, Scalaz._
-import nl.lumc.sasc.biopet.core._
-import nl.lumc.sasc.biopet.core.config._
-
-class Fastqc(val root: Configurable) extends BiopetCommandLineFunction {
-
- @Input(doc = "Contaminants", required = false)
- var contaminants: File = _
-
- @Input(doc = "Fastq file", shortName = "FQ")
- var fastqfile: File = _
-
- @Output(doc = "Output", shortName = "out")
- var output: File = _
-
- executable = config("exe", default = "fastqc")
- var java_exe: String = config("exe", default = "java", submodule = "java")
- var kmers: Option[Int] = config("kmers")
- var quiet: Boolean = config("quiet")
- var noextract: Boolean = config("noextract")
- var nogroup: Boolean = config("nogroup")
- var extract: Boolean = config("extract", default = true)
-
- override val versionRegex = """FastQC (.*)""".r
- override val defaultThreads = 4
-
- override def afterGraph {
- this.checkExecutable
- if (contaminants == null) {
- val fastqcDir = executable.substring(0, executable.lastIndexOf("/"))
- contaminants = new File(fastqcDir + "/Contaminants/contaminant_list.txt")
- }
- }
-
- override def versionCommand = executable + " --version"
-
- def cmdLine = {
- required(executable) +
- optional("--java", java_exe) +
- optional("--threads", threads) +
- optional("--contaminants", contaminants) +
- optional("--kmers", kmers) +
- conditional(nogroup, "--nogroup") +
- conditional(noextract, "--noextract") +
- conditional(extract, "--extract") +
- conditional(quiet, "--quiet") +
- required("-o", output.getParent()) +
- required(fastqfile)
- }
-
+class Fastqc(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Fastqc(root) {
def getDataBlock(name: String): Array[String] = { // Based on Fastqc v0.10.1
val outputDir = output.getName.stripSuffix(".zip")
val dataFile = new File(outputDir + "/fastqc_data.txt")
diff --git a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
index 6f785f7ecf2e21637b14144f9040160215d26e16..031eab73432bddb1d769e1d6fce2c7f3cab60cfd 100644
--- a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
+++ b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
@@ -1,17 +1,11 @@
package nl.lumc.sasc.biopet.pipelines.flexiprep
-import scala.util.parsing.json._
-
import org.broadinstitute.gatk.queue.QScript
-import org.broadinstitute.gatk.queue.extensions.gatk._
-import org.broadinstitute.gatk.queue.extensions.picard._
-import org.broadinstitute.gatk.queue.function._
import org.broadinstitute.gatk.utils.commandline.{ Input, Argument }
-import nl.lumc.sasc.biopet.core._
-import nl.lumc.sasc.biopet.core.config._
-import nl.lumc.sasc.biopet.extensions._
-import nl.lumc.sasc.biopet.extensions.fastq._
+import nl.lumc.sasc.biopet.core.{BiopetQScript, PipelineCommand}
+import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.extensions.{Cat, Ln, Pbzip2, Sha1sum, Zcat}
import nl.lumc.sasc.biopet.pipelines.flexiprep.scripts._
class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
diff --git a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepSummary.scala b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepSummary.scala
index d5d8effd3e7cc8e9a39023cee997106309e8b3b1..915c17fcc07db8ebfba06553996bd9faeedbdeca 100644
--- a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepSummary.scala
+++ b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepSummary.scala
@@ -2,10 +2,7 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.extensions.Sha1sum
-import nl.lumc.sasc.biopet.extensions.fastq.Cutadapt
-import nl.lumc.sasc.biopet.extensions.fastq.Fastqc
-import nl.lumc.sasc.biopet.extensions.fastq.Sickle
-import nl.lumc.sasc.biopet.pipelines.flexiprep.scripts.FastqSync
+import nl.lumc.sasc.biopet.pipelines.flexiprep.scripts.{ FastqSync, Seqstat }
import nl.lumc.sasc.biopet.pipelines.flexiprep.scripts.Seqstat
import org.broadinstitute.gatk.queue.function.InProcessFunction
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
diff --git a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Sickle.scala b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Sickle.scala
new file mode 100644
index 0000000000000000000000000000000000000000..1e2477aeea31e5b757dfcce664813f245b9d63dc
--- /dev/null
+++ b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Sickle.scala
@@ -0,0 +1,49 @@
+/*
+ * To change this license header, choose License Headers in Project Properties.
+ * To change this template file, choose Tools | Templates
+ * and open the template in the editor.
+ */
+
+package nl.lumc.sasc.biopet.pipelines.flexiprep
+
+import java.io.File
+import nl.lumc.sasc.biopet.core.config.Configurable
+import scala.io.Source
+
+import org.broadinstitute.gatk.utils.commandline.{ Input }
+
+
+import argonaut._, Argonaut._
+import scalaz._, Scalaz._
+
+class Sickle(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Sickle(root) {
+ @Input(doc = "qualityType file", required = false)
+ var qualityTypeFile: File = _
+
+ override def beforeCmd {
+ super.beforeCmd
+ qualityType = getQualityTypeFromFile
+ }
+
+ def getQualityTypeFromFile: String = {
+ if (qualityType == null && qualityTypeFile != null) {
+ if (qualityTypeFile.exists()) {
+ for (line <- Source.fromFile(qualityTypeFile).getLines) {
+ var s: String = line.substring(0, line.lastIndexOf("\t"))
+ return s
+ }
+ } else logger.warn("File : " + qualityTypeFile + " does not exist")
+ }
+ return null
+ }
+
+ def getSummary: Json = {
+ return jNull
+ }
+}
+
+object Sickle {
+ def mergeSummarys(jsons: List[Json]): Json = {
+ return jNull
+ }
+}
\ No newline at end of file
diff --git a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Seqstat.scala b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Seqstat.scala
index f2ad9ae8be05b6ce163125a8f7969ec078b89fc0..9fda06f73121b66b9a30273fb04d4399c5cacc1b 100644
--- a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Seqstat.scala
+++ b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Seqstat.scala
@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep.scripts
import java.io.File
-import nl.lumc.sasc.biopet.extensions.fastq.Fastqc
+import nl.lumc.sasc.biopet.pipelines.flexiprep.Fastqc
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import argonaut._, Argonaut._
@@ -32,7 +32,6 @@ class Seqstat(val root: Configurable) extends PythonCommandLineFunction {
case s if (s.contains("Illumina <1.3")) => fmt = "solexa"
case s if (s.contains("Illumina 1.3")) => fmt = "illumina"
case s if (s.contains("Illumina 1.5")) => fmt = "illumina"
- //case _ => null
}
}
}
diff --git a/mapping/nbactions.xml b/mapping/nbactions.xml
index ee04c09654afac7153f7dfcc062a60ee5d4db617..f1dfa5fc5ad1a76733f10543bf48af3b1583331d 100644
--- a/mapping/nbactions.xml
+++ b/mapping/nbactions.xml
@@ -10,7 +10,7 @@
<goal>org.codehaus.mojo:exec-maven-plugin:1.2.1:exec</goal>
</goals>
<properties>
- <exec.args>-classpath %classpath nl.lumc.sasc.biopet.pipelines.mapping.Mapping -R1 /data/DIV5/SASC/pjvan_thof/rig_validation/input/gcat_set_025/gcat_set_025_1.fastq.gz -R2 /data/DIV5/SASC/pjvan_thof/rig_validation/input/gcat_set_025/gcat_set_025_2.fastq.gz -outputDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/mapping/examples/test.json -RGLB test -RGSM test -ALN bwa -l DEBUG</exec.args>
+ <exec.args>-classpath %classpath nl.lumc.sasc.biopet.pipelines.mapping.Mapping -R1 /data/DIV5/SASC/pjvan_thof/rig_validation/input/gcat_set_025/gcat_set_025_1.fastq.gz -R2 /data/DIV5/SASC/pjvan_thof/rig_validation/input/gcat_set_025/gcat_set_025_2.fastq.gz -outDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/mapping/examples/test.json -RGLB test -RGSM test -ALN bwa -l DEBUG</exec.args>
<exec.executable>java</exec.executable>
<exec.workingdir>/home/pjvan_thof/pipelines/test</exec.workingdir>
</properties>
@@ -25,7 +25,7 @@
<goal>org.codehaus.mojo:exec-maven-plugin:1.2.1:exec</goal>
</goals>
<properties>
- <exec.args>-Xdebug -Xrunjdwp:transport=dt_socket,server=n,address=${jpda.address} -classpath %classpath nl.lumc.sasc.biopet.pipelines.mapping.Mapping -R1 /data/DIV5/SASC/pjvan_thof/rig_validation/input/gcat_set_025/gcat_set_025_1.fastq.gz -R2 /data/DIV5/SASC/pjvan_thof/rig_validation/input/gcat_set_025/gcat_set_025_2.fastq.gz -outputDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/mapping/examples/test.json -RGLB test -RGSM test -ALN bwa -l DEBUG</exec.args>
+ <exec.args>-Xdebug -Xrunjdwp:transport=dt_socket,server=n,address=${jpda.address} -classpath %classpath nl.lumc.sasc.biopet.pipelines.mapping.Mapping -R1 /data/DIV5/SASC/pjvan_thof/rig_validation/input/gcat_set_025/gcat_set_025_1.fastq.gz -R2 /data/DIV5/SASC/pjvan_thof/rig_validation/input/gcat_set_025/gcat_set_025_2.fastq.gz -outDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/mapping/examples/test.json -RGLB test -RGSM test -ALN bwa -l DEBUG</exec.args>
<exec.executable>java</exec.executable>
<jpda.listen>true</jpda.listen>
<exec.workingdir>/home/pjvan_thof/pipelines/test</exec.workingdir>
@@ -41,7 +41,7 @@
<goal>org.codehaus.mojo:exec-maven-plugin:1.2.1:exec</goal>
</goals>
<properties>
- <exec.args>-classpath %classpath nl.lumc.sasc.biopet.pipelines.mapping.Mapping -R1 /data/DIV5/SASC/pjvan_thof/rig_validation/input/gcat_set_025/gcat_set_025_1.fastq.gz -R2 /data/DIV5/SASC/pjvan_thof/rig_validation/input/gcat_set_025/gcat_set_025_2.fastq.gz -outputDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/mapping/examples/test.json -RGLB test -RGSM test -ALN bwa -l DEBUG</exec.args>
+ <exec.args>-classpath %classpath nl.lumc.sasc.biopet.pipelines.mapping.Mapping -R1 /data/DIV5/SASC/pjvan_thof/rig_validation/input/gcat_set_025/gcat_set_025_1.fastq.gz -R2 /data/DIV5/SASC/pjvan_thof/rig_validation/input/gcat_set_025/gcat_set_025_2.fastq.gz -outDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/mapping/examples/test.json -RGLB test -RGSM test -ALN bwa -l DEBUG</exec.args>
<exec.executable>java</exec.executable>
<exec.workingdir>/home/pjvan_thof/pipelines/test</exec.workingdir>
</properties>