Commit 27035485 authored by bow's avatar bow
Browse files

Merge branch 'patch-carp' into 'develop'

Patch carp

Merge to fix the wrong directory of MACS2 single samples runs

See merge request !113
parents 1571f046 09103695
......@@ -44,7 +44,7 @@ class IGVToolsCount(val root: Configurable) extends IGVTools {
var pairs: Boolean = config("pairs", default = false)
override val defaultVmem = "4G"
override val defaultVmem = "6G"
override def beforeGraph {
super.beforeGraph
......
......@@ -81,7 +81,7 @@ class Macs2CallPeak(val root: Configurable) extends Macs2 {
conditional(verbose, "--verbose") + /* Whether to output verbosely */
optional("--tsize", tsize) + /* Sets custom tag length, if not specified macs will use first 10 sequences to estimate the size */
optional("--bw", bandwith) + /* The bandwith to use for model building. Set this parameter as the sonication fragment size estimated in the wetlab */
optional("'--mfold'", repeat(mfold), escape = false) + /* The parameter to select regions within the model fold. Must be a upper and lower limit. */
(if (mfold.isEmpty) "" else optional("'--mfold'", repeat(mfold), escape = false)) + /* The parameter to select regions within the model fold. Must be a upper and lower limit. */
conditional(fixbimodel, "--fix-bimodal") + /* Whether turn on the auto paired-peak model process. If it's set, when MACS failed to build paired model, it will use the nomodel settings, the '--extsize' parameter to extend each tags. If set, MACS will be terminated if paried-peak model is failed. */
conditional(nomodel, "--nomodel") + /* While on, MACS will bypass building the shifting model */
optional("--shift", shift) + /* You can set an arbitrary shift in basepairs here */
......
......@@ -38,8 +38,8 @@ class Seqstat(val root: Configurable) extends BiopetJavaCommandLineFunction with
@Output(doc = "Output JSON", shortName = "output", required = true)
var output: File = null
override val defaultVmem = "4G"
memoryLimit = Option(3.0)
override val defaultVmem = "3G"
memoryLimit = Option(1.0)
override def commandLine = super.commandLine + required("-i", input) + " > " + required(output)
......
......@@ -110,7 +110,7 @@ class Carp(val root: Configurable) extends QScript with MultiSampleQScript with
val macs2 = new Macs2CallPeak(qscript)
macs2.treatment = bamFile
macs2.name = Some(sampleId)
macs2.outputdir = sampleDir + "macs2/" + sampleId + "/"
macs2.outputdir = sampleDir + File.separator + "macs2" + File.separator + sampleId + File.separator
add(macs2)
}
}
......@@ -137,7 +137,7 @@ class Carp(val root: Configurable) extends QScript with MultiSampleQScript with
macs2.treatment = sample.bamFile
macs2.control = samples(controlId).bamFile
macs2.name = Some(sampleId + "_VS_" + controlId)
macs2.outputdir = sample.sampleDir + "/" + "macs2/" + macs2.name.get + "/"
macs2.outputdir = sample.sampleDir + File.separator + "macs2" + File.separator + macs2.name.get + File.separator
add(macs2)
}
}
......
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