From 1caad8532e91460b82138cabd5c8ed764e0b8e19 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 20 Sep 2016 16:30:39 +0200
Subject: [PATCH] Add a split to unique reports
---
.../centrifuge/CentrifugeKreport.scala | 13 +++++++++++-
.../pipelines/gears/GearsCentrifuge.scala | 20 +++++++++++++------
.../biopet/pipelines/gears/GearsReport.scala | 7 +++++--
3 files changed, 31 insertions(+), 9 deletions(-)
diff --git a/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/centrifuge/CentrifugeKreport.scala b/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/centrifuge/CentrifugeKreport.scala
index 24cd283c3..386a372b3 100644
--- a/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/centrifuge/CentrifugeKreport.scala
+++ b/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/centrifuge/CentrifugeKreport.scala
@@ -19,10 +19,21 @@ class CentrifugeKreport(val root: Configurable) extends BiopetCommandLineFunctio
@Input(doc = "Centrifuge index prefix", required = true)
var index: File = config("centrifuge_index", namespace = "centrifuge")
+ var onlyUnique: Boolean = config ("only_unique", default = false)
+ var showZeros: Boolean = config ("show_zeros", default = false)
+ var isCounts: Boolean = config ("is_counts", default = false)
+
+ var minScore: Option[Double] = config("min_score")
+ var minLength: Option[Int] = config("min_length")
+
executable = config("exe", default = "centrifuge-kreport", freeVar = false)
def cmdLine = executable +
- //TODO: Options
+ conditional(onlyUnique, "--only-unique") +
+ conditional(showZeros, "--show-zeros") +
+ conditional(showZeros, "--is-counts") +
+ optional("--min-score=", minScore, spaceSeparated = false) +
+ optional("--min-length=", minLength, spaceSeparated = false) +
required("-x", index) +
repeat(centrifugeOutputFiles) +
" > " + required(output)
diff --git a/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsCentrifuge.scala b/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsCentrifuge.scala
index 45ecf3e60..210c53182 100644
--- a/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsCentrifuge.scala
+++ b/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsCentrifuge.scala
@@ -18,6 +18,8 @@ class GearsCentrifuge(val root: Configurable) extends QScript with SummaryQScrip
var outputName: String = _
+ override def fixedValues = Map("centrifugekreport" -> Map("only_unique" -> false))
+
def init(): Unit = {
require(fastqR1 != null)
if (outputName == null) outputName = fastqR1.getName
@@ -34,19 +36,25 @@ class GearsCentrifuge(val root: Configurable) extends QScript with SummaryQScrip
centrifuge.report = Some(new File(outputDir, s"$outputName.centrifuge.report"))
add(centrifuge)
+ makeKreport(List(centrifuge.output), "centrifuge", unique = false)
+ makeKreport(List(centrifuge.output), "centrifuge_unique", unique = true)
+
+ addSummaryJobs()
+ }
+
+ protected def makeKreport(inputFiles: List[File], name: String, unique: Boolean): Unit = {
val centrifugeKreport = new CentrifugeKreport(this)
- centrifugeKreport.centrifugeOutputFiles :+= centrifuge.output
- centrifugeKreport.output = new File(outputDir, s"$outputName.centrifuge.kreport")
+ centrifugeKreport.centrifugeOutputFiles = inputFiles
+ centrifugeKreport.output = new File(outputDir, s"$outputName.$name.kreport")
+ centrifugeKreport.onlyUnique = unique
add(centrifugeKreport)
val krakenReportJSON = new KrakenReportToJson(this)
krakenReportJSON.inputReport = centrifugeKreport.output
- krakenReportJSON.output = new File(outputDir, s"$outputName.krkn.json")
+ krakenReportJSON.output = new File(outputDir, s"$outputName.$name.krkn.json")
krakenReportJSON.skipNames = config("skipNames", default = false)
add(krakenReportJSON)
- addSummarizable(krakenReportJSON, "centrifuge_report")
-
- addSummaryJobs()
+ addSummarizable(krakenReportJSON, s"${name}_report")
}
/** Location of summary file */
diff --git a/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala b/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala
index bc38c3f32..69e005f26 100644
--- a/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala
+++ b/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala
@@ -46,8 +46,11 @@ object GearsReport extends MultisampleReportBuilder {
ReportPage(
(if (centrifugeExecuted) List("Centriguge analysis" -> ReportPage(List(), List(
- "Krona plot" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
- )), Map("summaryStatsTag" -> "centrifuge_report", "summaryModuleTag" -> "gearscentrifuge")))
+ "Unique Krona plot" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
+ Map("summaryStatsTag" -> "centrifuge_unique_report")
+ ), "All Krona plot" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
+ Map("summaryStatsTag" -> "centrifuge_report")
+ )), Map("summaryModuleTag" -> "gearscentrifuge")))
else Nil) ::: (if (krakenExecuted) List("Kraken analysis" -> ReportPage(List(), List(
"Krona plot" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
)), Map()))
--
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