Commit df582f1a authored by Peter van 't Hof's avatar Peter van 't Hof Committed by GitHub
Browse files

Merge pull request #167 from biopet/fix-BIOPET-755

Small fixes for Gentrap
parents 23bdc5b2 931771fe
...@@ -44,6 +44,8 @@ class RefflatStats(val parent: Configurable) extends ToolCommandFunction with Re ...@@ -44,6 +44,8 @@ class RefflatStats(val parent: Configurable) extends ToolCommandFunction with Re
@Output(required = true) @Output(required = true)
var intronOutput: File = _ var intronOutput: File = _
override def defaultCoreMemory = 5.0
override def beforeGraph(): Unit = { override def beforeGraph(): Unit = {
super.beforeGraph() super.beforeGraph()
if (reference == null) reference = referenceFasta() if (reference == null) reference = referenceFasta()
......
...@@ -80,8 +80,13 @@ class Star(val parent: Configurable) ...@@ -80,8 +80,13 @@ class Star(val parent: Configurable)
var genomeSAindexNbases: Option[Long] = config("genomesaindexnbases") var genomeSAindexNbases: Option[Long] = config("genomesaindexnbases")
var genomeSAsparseD: Option[Int] = config("genomesasparsed") var genomeSAsparseD: Option[Int] = config("genomesasparsed")
private def defaultGtf: Option[File] = config("annotation_gtf")
@Input(required = false) @Input(required = false)
var sjdbGTFfile: Option[File] = config("sjdbgtfile") var sjdbGTFfile: Option[File] = defaultGtf match {
case Some(file) => config("sjdbgtfile", default = file)
case _ => config("sjdbgtfile")
}
var sjdbGTFchrPrefix: Option[String] = config("sjdbgtfchrprefix") var sjdbGTFchrPrefix: Option[String] = config("sjdbgtfchrprefix")
var sjdbGTFfeatureExon: Option[String] = config("sjdbgtffeatureexon") var sjdbGTFfeatureExon: Option[String] = config("sjdbgtffeatureexon")
var sjdbGTFtagExonParentTranscript: Option[String] = config("sjdbgtftagexonparenttranscript") var sjdbGTFtagExonParentTranscript: Option[String] = config("sjdbgtftagexonparenttranscript")
......
...@@ -31,16 +31,17 @@ object ValidateAnnotation extends ToolCommand { ...@@ -31,16 +31,17 @@ object ValidateAnnotation extends ToolCommand {
gtfFiles: List[File] = Nil) gtfFiles: List[File] = Nil)
class OptParser extends AbstractOptParser[Args](commandName) { class OptParser extends AbstractOptParser[Args](commandName) {
opt[File]('r', "refflatFile") maxOccurs 1 valueName "<file>" action { (x, c) => opt[File]('r', "refflatFile") unbounded () maxOccurs 1 valueName "<file>" action { (x, c) =>
c.copy(refflatFile = Some(x)) c.copy(refflatFile = Some(x))
} text "Refflat file to check" } text "Refflat file to check"
opt[File]('g', "gtfFile") valueName "<file>" action { (x, c) => opt[File]('g', "gtfFile") unbounded () valueName "<file>" action { (x, c) =>
c.copy(gtfFiles = x :: c.gtfFiles) c.copy(gtfFiles = x :: c.gtfFiles)
} text "Gtf files to check" } text "Gtf files to check"
opt[File]('R', "reference") required () maxOccurs 1 valueName "<file>" action { (x, c) => opt[File]('R', "reference") unbounded () required () maxOccurs 1 valueName "<file>" action {
c.copy(reference = x) (x, c) =>
c.copy(reference = x)
} text "Reference fasta to check vcf file against" } text "Reference fasta to check vcf file against"
opt[Unit]("disableFail") maxOccurs 1 valueName "<file>" action { (_, c) => opt[Unit]("disableFail") unbounded () maxOccurs 1 valueName "<file>" action { (_, c) =>
c.copy(failOnError = false) c.copy(failOnError = false)
} text "Do not fail on error. The tool will still exit when encountering an error, but will do so with exit code 0" } text "Do not fail on error. The tool will still exit when encountering an error, but will do so with exit code 0"
} }
......
...@@ -54,7 +54,7 @@ trait Measurement extends SummaryQScript with Reference { qscript: QScript => ...@@ -54,7 +54,7 @@ trait Measurement extends SummaryQScript with Reference { qscript: QScript =>
require(bamFiles.nonEmpty) require(bamFiles.nonEmpty)
} }
lazy val mergeCountFiles: Boolean = config("merge_count_files", default = true) lazy val mergeCountFiles: Boolean = config("merge_count_files", default = bamFiles.size > 1)
private var extraSummaryFiles: Map[String, File] = Map() private var extraSummaryFiles: Map[String, File] = Map()
......
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