Commit 78159ed9 authored by Peter van 't Hof's avatar Peter van 't Hof

trying to fix weird error in testing

parent 261ebe2a
...@@ -154,6 +154,7 @@ class BamMetrics(val parent: Configurable) extends QScript ...@@ -154,6 +154,7 @@ class BamMetrics(val parent: Configurable) extends QScript
val biStrict = BedtoolsIntersect(this, inputBam, intervals.bed, val biStrict = BedtoolsIntersect(this, inputBam, intervals.bed,
output = new File(targetDir, inputBam.getName.stripSuffix(".bam") + ".overlap.strict.sam"), output = new File(targetDir, inputBam.getName.stripSuffix(".bam") + ".overlap.strict.sam"),
minOverlap = config("strict_intersect_overlap", default = 1.0)) minOverlap = config("strict_intersect_overlap", default = 1.0))
biStrict.jobOutputFile = new File(targetDir, ".biStrict.Bedtools.out")
val biopetFlagstatStrict = BiopetFlagstat(this, biStrict.output, targetDir) val biopetFlagstatStrict = BiopetFlagstat(this, biStrict.output, targetDir)
addSummarizable(biopetFlagstatStrict, targetName + "_flagstats_strict") addSummarizable(biopetFlagstatStrict, targetName + "_flagstats_strict")
add(new BiopetFifoPipe(this, List(biStrict, biopetFlagstatStrict))) add(new BiopetFifoPipe(this, List(biStrict, biopetFlagstatStrict)))
...@@ -161,6 +162,7 @@ class BamMetrics(val parent: Configurable) extends QScript ...@@ -161,6 +162,7 @@ class BamMetrics(val parent: Configurable) extends QScript
val biLoose = BedtoolsIntersect(this, inputBam, intervals.bed, val biLoose = BedtoolsIntersect(this, inputBam, intervals.bed,
output = new File(targetDir, inputBam.getName.stripSuffix(".bam") + ".overlap.loose.sam"), output = new File(targetDir, inputBam.getName.stripSuffix(".bam") + ".overlap.loose.sam"),
minOverlap = config("loose_intersect_overlap", default = 0.01)) minOverlap = config("loose_intersect_overlap", default = 0.01))
biLoose.jobOutputFile = new File(targetDir, ".biLoose.Bedtools.out")
val biopetFlagstatLoose = BiopetFlagstat(this, biLoose.output, targetDir) val biopetFlagstatLoose = BiopetFlagstat(this, biLoose.output, targetDir)
addSummarizable(biopetFlagstatLoose, targetName + "_flagstats_loose") addSummarizable(biopetFlagstatLoose, targetName + "_flagstats_loose")
add(new BiopetFifoPipe(this, List(biLoose, biopetFlagstatLoose))) add(new BiopetFifoPipe(this, List(biLoose, biopetFlagstatLoose)))
......
...@@ -23,13 +23,13 @@ import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output } ...@@ -23,13 +23,13 @@ import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
class BedtoolsIntersect(val parent: Configurable) extends Bedtools { class BedtoolsIntersect(val parent: Configurable) extends Bedtools {
@Input(doc = "Input file (bed/gff/vcf/bam)") @Input(doc = "Input file (bed/gff/vcf/bam)")
var input: File = null var input: File = _
@Input(doc = "Intersect file (bed/gff/vcf)") @Input(doc = "Intersect file (bed/gff/vcf)")
var intersectFile: File = null var intersectFile: File = _
@Output(doc = "output File") @Output(doc = "output File")
var output: File = null var output: File = _
@Argument(doc = "Min overlap", required = false) @Argument(doc = "Min overlap", required = false)
var minOverlap: Option[Double] = config("minoverlap") var minOverlap: Option[Double] = config("minoverlap")
...@@ -46,7 +46,8 @@ class BedtoolsIntersect(val parent: Configurable) extends Bedtools { ...@@ -46,7 +46,8 @@ class BedtoolsIntersect(val parent: Configurable) extends Bedtools {
} }
/** Returns command to execute */ /** Returns command to execute */
def cmdLine = required(executable) + required("intersect") + def cmdLine: String = required(executable) +
required("intersect") +
required(inputTag, input) + required(inputTag, input) +
required("-b", intersectFile) + required("-b", intersectFile) +
optional("-f", minOverlap) + optional("-f", minOverlap) +
......
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