Commit af8d9361 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Simplify modules

parent 5c344be9
......@@ -83,9 +83,7 @@ class GearsSingle(val root: Configurable) extends QScript with SummaryQScript wi
extract.outputDir = outputDir
extract.bamFile = bam
extract.outputName = outputName
extract.init()
extract.biopetScript()
addAll(extract.functions)
add(extract)
(extract.fastqUnmappedR1, Some(extract.fastqUnmappedR2))
case _ => throw new IllegalArgumentException("Missing input files")
}
......@@ -94,10 +92,7 @@ class GearsSingle(val root: Configurable) extends QScript with SummaryQScript wi
flexiprep.input_R1 = r1
flexiprep.input_R2 = r2
flexiprep.outputDir = new File(outputDir, "flexiprep")
flexiprep.init()
flexiprep.biopetScript()
addAll(flexiprep.functions)
addSummaryQScript(flexiprep)
add(flexiprep)
if (gearsUseKraken) {
val kraken = new GearsKraken(this)
......@@ -105,10 +100,7 @@ class GearsSingle(val root: Configurable) extends QScript with SummaryQScript wi
kraken.fastqR1 = flexiprep.fastqR1Qc
kraken.fastqR2 = flexiprep.fastqR2Qc
kraken.outputName = outputName
kraken.init()
kraken.biopetScript()
addAll(kraken.functions)
addSummaryQScript(kraken)
add(kraken)
}
if (gearsUserQiimeRtax) {
......@@ -116,9 +108,7 @@ class GearsSingle(val root: Configurable) extends QScript with SummaryQScript wi
qiimeRatx.outputDir = new File(outputDir, "qiime_rtax")
qiimeRatx.fastqR1 = flexiprep.fastqR1Qc
qiimeRatx.fastqR2 = flexiprep.fastqR2Qc
qiimeRatx.init()
qiimeRatx.biopetScript()
addAll(qiimeRatx.functions)
add(qiimeRatx)
}
if (gearsUserQiimeClosed) {
......@@ -126,9 +116,7 @@ class GearsSingle(val root: Configurable) extends QScript with SummaryQScript wi
qiimeClosed.outputDir = new File(outputDir, "qiime_rtax")
qiimeClosed.fastqR1 = flexiprep.fastqR1Qc
qiimeClosed.fastqR2 = flexiprep.fastqR2Qc
qiimeClosed.init()
qiimeClosed.biopetScript()
addAll(qiimeClosed.functions)
add(qiimeClosed)
}
addSummaryJobs()
......
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