diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/TopHat.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Tophat.scala
similarity index 68%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/TopHat.scala
rename to public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Tophat.scala
index ce86a1ed9bd1e8d1afa04867887be2f21cf6231b..7cca2fc1aa21642844687329fd1c30082b19101a 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/TopHat.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Tophat.scala
@@ -22,20 +22,28 @@ import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
class TopHat(val root: Configurable) extends BiopetCommandLineFunction {
- @Input(doc = "FastQ file R1", shortName = "R1")
- var R1: File = _
- @Input(doc = "FastQ file R2", shortName = "R2", required = false)
- var R2: File = _
+ @Input(doc = "FastQ file(s) R1", shortName = "R1")
+ var R1: List[File] = List.empty[File]
- @Input(doc = "Bowtie index", shortName = "bti")
- var bowtie_index: File = config("bowtie_index")
+ @Input(doc = "FastQ file(s) R2", shortName = "R2", required = false)
+ var R2: List[File] = List.empty[File]
- @Argument(doc = "Output Directory")
- var outputDir: String = _
+ /** output files, computed automatically from output directory */
- @Output(doc = "Output file SAM", shortName = "output")
- var output: File = _
+ @Output(doc = "Output SAM/BAM file")
+ lazy val outputGtf: File = {
+ require(R1.nonEmpty && output_dir != null,
+ "Read 1 input(s) are defined and output directory is defined")
+ // cufflinks always outputs a transcripts.gtf file in the output directory
+ new File(output_dir, "accepted_hits.bam")
+ }
+
+ @Argument(doc = "Bowtie index", shortName = "bti", required = true)
+ var bowtie_index: String = config("bowtie_index")
+
+ /** write all output files to this directory [./] */
+ var output_dir: File = config("output_dir", default = new File("tophat_out"))
// options set via API or config
// var numrecords: String = config("numrecords", default = "all")
@@ -56,25 +64,18 @@ class TopHat(val root: Configurable) extends BiopetCommandLineFunction {
// var logfile: String = config("logfile")
executable = config("exe", default = "tophat", freeVar = false)
+
override val versionRegex = """TopHat v(.*)""".r
override val versionExitcode = List(0, 1)
+ override def versionCommand = executable + " --version"
override val defaultVmem = "4G"
override val defaultThreads = 8
- override def versionCommand = executable + " --version"
-
- override def beforeGraph() {
- if (!outputDir.endsWith("/")) outputDir += "/"
- output = new File(outputDir + "accepted_hits.bam")
- }
+ //override def beforeGraph = {}
- def cmdLine: String = {
- var cmd: String = required(executable) +
- optional("-p", nCoresRequest) +
- "--no-convert-bam" +
- required(bowtie_index) +
- required(R1) + optional(R2)
- return cmd
- }
+ def cmdLine: String = required(executable) +
+ required(bowtie_index) +
+ required(R1.mkString(",")) +
+ optional(R2.mkString(","))
}
diff --git a/public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/templates/pdf/img/gentrap_front.png b/public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/templates/pdf/gentrap_front.png
similarity index 100%
rename from public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/templates/pdf/img/gentrap_front.png
rename to public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/templates/pdf/gentrap_front.png
diff --git a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/PdfReportTemplateWriter.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/PdfReportTemplateWriter.scala
index 490b0e4e81b5b3e6226dc1662d8673514cbaaf94..508ce707b6186657e8258d32a2d2d01010407b6b 100644
--- a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/PdfReportTemplateWriter.scala
+++ b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/PdfReportTemplateWriter.scala
@@ -6,9 +6,9 @@
package nl.lumc.sasc.biopet.pipelines.gentrap.scripts
-import java.io.File
+import java.io.{ File, FileOutputStream }
-import org.apache.commons.io.FileUtils
+import org.apache.commons.io.IOUtils
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import nl.lumc.sasc.biopet.core.config.Configurable
@@ -19,10 +19,6 @@ import nl.lumc.sasc.biopet.extensions.PythonCommandLineFunction
*/
class PdfReportTemplateWriter(val root: Configurable) extends PythonCommandLineFunction {
- val templateResDir: File = new File(getClass.getResource("/nl/lumc/sasc/biopet/pipelines/gentrap/templates/pdf").toURI)
- val templateWorkDir: File = new File(".queue/tmp/nl/lumc/sasc/biopet/pipelines/gentrap/templates/pdf")
- val imgWorkDir: File = new File(templateWorkDir, "img")
-
@Input(doc = "Input summary file", required = true)
var summaryFile: File = null
@@ -30,13 +26,34 @@ class PdfReportTemplateWriter(val root: Configurable) extends PythonCommandLineF
def mainTemplateFile: File = new File(templateWorkDir, "main.tex")
@Input(doc = "Main report logo", required = true) // def since we hard-code the logo
- def logoFile: File = new File(imgWorkDir, "gentrap_front.png")
+ def logoFile: File = new File(templateWorkDir, "gentrap_front.png")
@Output(doc = "Output file", required = true)
var output: File = null
- protected def prepTemplate(): Unit = {
- FileUtils.copyDirectory(templateResDir, templateWorkDir)
+ val templateWorkDir: File = new File(".queue/tmp/nl/lumc/sasc/biopet/pipelines/gentrap/templates/pdf")
+ val templateFiles: Seq[String] = Seq(
+ "main.tex", "gentrap_front.png",
+ "sample.tex", "sample_mapping.tex",
+ "lib.tex", "lib_seqeval.tex", "lib_mapping.tex"
+ )
+
+ protected def prepTemplate(name: String,
+ subPackage: String = "/nl/lumc/sasc/biopet/pipelines/gentrap/templates/pdf"): Unit = {
+ val target = new File(".queue/tmp" + subPackage, name)
+ if (!target.getParentFile.exists) target.getParentFile.mkdirs()
+ val is = getClass.getResourceAsStream(subPackage + "/" + name)
+ val os = new FileOutputStream(target)
+ org.apache.commons.io.IOUtils.copy(is, os)
+ os.close()
+
+ //python_script_name = script
+ //python_script = new File(".queue/tmp/" + subpackage + python_script_name)
+ //if (!python_script.getParentFile.exists) python_script.getParentFile.mkdirs
+ //val is = getClass.getResourceAsStream(subpackage + python_script_name)
+ //val os = new FileOutputStream(python_script)
+ //org.apache.commons.io.IOUtils.copy(is, os)
+ //os.close()
}
def cmdLine = {
@@ -48,5 +65,5 @@ class PdfReportTemplateWriter(val root: Configurable) extends PythonCommandLineF
}
setPythonScript("pdf_report.py")
- prepTemplate()
+ templateFiles.foreach(t => prepTemplate(t))
}