Commit 0a25827e authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Expose subpipelines

parent 9c1384fb
......@@ -40,9 +40,9 @@ class GearsSingle(val root: Configurable) extends QScript with SummaryQScript wi
@Argument(required = false)
var outputName: String = _
var gearsUseKraken: Boolean = config("gears_use_kraken", default = true)
var gearsUserQiimeRtax: Boolean = config("gear_use_qiime_rtax", default = false)
var gearsUserQiimeClosed: Boolean = config("gear_use_qiime_closed", default = false)
val krakenScript = if (config("gears_use_kraken", default = true)) Some(new GearsKraken(this)) else None
val qiimeRatx = if (config("gear_use_qiime_rtax", default = false)) Some(new GearsQiimeRtax(this)) else None
val qiimeClosed = if (config("gear_use_qiime_closed", default = false)) Some(new GearsQiimeClosed(this)) else None
/** Executed before running the script */
def init(): Unit = {
......@@ -93,8 +93,7 @@ class GearsSingle(val root: Configurable) extends QScript with SummaryQScript wi
flexiprep.outputDir = new File(outputDir, "flexiprep")
add(flexiprep)
if (gearsUseKraken) {
val kraken = new GearsKraken(this)
krakenScript foreach { kraken =>
kraken.outputDir = new File(outputDir, "kraken")
kraken.fastqR1 = flexiprep.fastqR1Qc
kraken.fastqR2 = flexiprep.fastqR2Qc
......@@ -102,16 +101,14 @@ class GearsSingle(val root: Configurable) extends QScript with SummaryQScript wi
add(kraken)
}
if (gearsUserQiimeRtax) {
val qiimeRatx = new GearsQiimeRtax(this)
qiimeRatx foreach { qiimeRatx =>
qiimeRatx.outputDir = new File(outputDir, "qiime_rtax")
qiimeRatx.fastqR1 = flexiprep.fastqR1Qc
qiimeRatx.fastqR2 = flexiprep.fastqR2Qc
add(qiimeRatx)
}
if (gearsUserQiimeClosed) {
val qiimeClosed = new GearsQiimeClosed(this)
qiimeClosed foreach { qiimeClosed =>
qiimeClosed.outputDir = new File(outputDir, "qiime_closed")
qiimeClosed.fastqR1 = flexiprep.fastqR1Qc
qiimeClosed.fastqR2 = flexiprep.fastqR2Qc
......
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