From 211b5e1891986efb55cc66d6b20bff2f268a6aa3 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Fri, 25 Dec 2015 14:31:39 +0100
Subject: [PATCH] Added merge output of qiimeClosed
---
.../sasc/biopet/pipelines/gears/Gears.scala | 27 ++++++++++++-------
1 file changed, 18 insertions(+), 9 deletions(-)
diff --git a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala b/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala
index 523465e13..ac38cb34c 100644
--- a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala
+++ b/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala
@@ -36,6 +36,16 @@ class Gears(val root: Configurable) extends QScript with MultiSampleQScript { qs
addSummaryJobs()
}
+ def qiimeClosedDir: Option[File] = {
+ if (samples.values.flatMap(_.gs.qiimeClosed).nonEmpty) {
+ Some(new File(outputDir, "qiime_closed_reference"))
+ } else None
+
+ }
+
+ def qiimeClosedOtuTable: Option[File] = qiimeClosedDir.map(new File(_, "otu_table.biom"))
+ def qiimeClosedOtuMap: Option[File] = qiimeClosedDir.map(new File(_, "otu_map.txt"))
+
/**
* Method where the multisample jobs should be added, this will be executed only when running the -sample argument is not given.
*/
@@ -45,24 +55,20 @@ class Gears(val root: Configurable) extends QScript with MultiSampleQScript { qs
val closedOtuMaps = gss.map(_.otuMap)
require(closedOtuTables.size == closedOtuMaps.size)
if (closedOtuTables.nonEmpty) {
- val closedDir = new File(outputDir, "qiime_closed_reference")
- val closedOtuTable = new File(closedDir, "otu_table.biom")
- val closedOtuMap = new File(closedDir, "otu_map.txt")
-
if (closedOtuTables.size > 1) {
val mergeTables = new MergeOtuTables(qscript)
mergeTables.input = closedOtuTables
- mergeTables.outputFile = closedOtuTable
+ mergeTables.outputFile = qiimeClosedOtuTable.get
add(mergeTables)
val mergeMaps = new MergeOtuMaps(qscript)
mergeMaps.input = closedOtuMaps
- mergeMaps.output = closedOtuMap
+ mergeMaps.output = qiimeClosedOtuMap.get
add(mergeMaps)
} else {
- add(Ln(qscript, closedOtuMaps.head, closedOtuMap))
- add(Ln(qscript, closedOtuTables.head, closedOtuTable))
+ add(Ln(qscript, closedOtuMaps.head, qiimeClosedOtuMap.get))
+ add(Ln(qscript, closedOtuTables.head, qiimeClosedOtuTable.get))
}
//TODO: Plots
@@ -149,7 +155,10 @@ class Gears(val root: Configurable) extends QScript with MultiSampleQScript { qs
def summarySettings: Map[String, Any] = Map()
/** File to put in the summary for thie pipeline */
- def summaryFiles: Map[String, File] = Map()
+ def summaryFiles: Map[String, File] = (
+ qiimeClosedOtuTable.map("qiime_closed_otu_table" -> _) ++
+ qiimeClosedOtuMap.map("qiime_closed_otu_map" -> _)
+ ).toMap
}
object Gears extends PipelineCommand
\ No newline at end of file
--
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