Commit 92dc5c59 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Removed config file reading, already done in biopetQScript

parent d2f9c54e
......@@ -26,7 +26,6 @@ class BamMetrics(val root: Configurable) extends QScript with BiopetQScript {
var wholeGenome = false
def init() {
for (file <- configfiles) globalConfig.loadConfigFile(file)
if (outputDir == null) throw new IllegalStateException("Missing Output directory on BamMetrics module")
else if (!outputDir.endsWith("/")) outputDir += "/"
if (config.contains("target_bed")) {
......
......@@ -43,7 +43,6 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
val summary = new FlexiprepSummary(this)
def init() {
for (file <- configfiles) globalConfig.loadConfigFile(file)
if (!skipTrim) skipTrim = config("skiptrim", default = false)
if (!skipClip) skipClip = config("skipclip", default = false)
if (input_R1 == null) throw new IllegalStateException("Missing R1 on flexiprep module")
......
......@@ -69,7 +69,7 @@ class Gentrap(val root: Configurable) extends QScript with BiopetQScript {
var cExonBase: Boolean = _
def init() {
for (file <- configfiles) globalConfig.loadConfigFile(file)
}
def biopetScript() {
......
......@@ -81,7 +81,6 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
val flexiprep = new Flexiprep(this)
def init() {
for (file <- configfiles) globalConfig.loadConfigFile(file)
if (aligner == null) aligner = config("aligner", default = defaultAligner)
if (reference == null) reference = config("reference")
if (outputDir == null) throw new IllegalStateException("Missing Output directory on mapping module")
......
......@@ -34,7 +34,6 @@ class Yamsvp(val root: Configurable) extends QScript with MultiSampleQScript {
}
override def init() {
for (file <- configfiles) globalConfig.loadConfigFile(file)
reference = config("reference", required = true)
if (outputDir == null)
throw new IllegalStateException("Output directory is not specified in the config / argument")
......
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