From 83c0d1eef9da65df18cbbe6f76200592568f9581 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Thu, 17 Dec 2015 17:31:08 +0100
Subject: [PATCH] Added merge of otu tables and maps
---
.../sasc/biopet/pipelines/gears/Gears.scala | 70 +++++++++++++++++--
1 file changed, 65 insertions(+), 5 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 95776672e..3f10af4cc 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
@@ -1,6 +1,10 @@
package nl.lumc.sasc.biopet.pipelines.gears
+import java.io.File
+
import nl.lumc.sasc.biopet.core.{ PipelineCommand, MultiSampleQScript }
+import nl.lumc.sasc.biopet.extensions.Ln
+import nl.lumc.sasc.biopet.extensions.qiime.MergeOtuTables
import nl.lumc.sasc.biopet.utils.Logging
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.QScript
@@ -35,6 +39,33 @@ class Gears(val root: Configurable) extends QScript with MultiSampleQScript { qs
* Method where the multisample jobs should be added, this will be executed only when running the -sample argument is not given.
*/
def addMultiSampleJobs(): Unit = {
+ val closedOtuTables = samples.values.flatMap(_.closedOtuTable).toList
+ val closedOtuMaps = samples.values.flatMap(_.closedOtuMap).toList
+ require(closedOtuTables.size == closedOtuMaps.size)
+ if (closedOtuTables.nonEmpty) {
+ val closedDir = new File(outputDir, "qiime_closed_reference")
+ val closedOtuTable = new File(closedDir, "closed.biom")
+ val closedOtuMap = new File(closedDir, "closed.map.txt")
+
+ if (closedOtuTables.size > 1) {
+ val mergeTables = new MergeOtuTables(qscript)
+ mergeTables.input = closedOtuTables
+ mergeTables.outputFile = closedOtuTable
+ add(mergeTables)
+
+ val mergeMaps = new MergeOtuTables(qscript)
+ mergeMaps.input = closedOtuMaps
+ mergeMaps.outputFile = closedOtuMap
+ add(mergeMaps)
+
+ } else {
+ add(Ln(qscript, closedOtuMaps.head, closedOtuMap))
+ add(Ln(qscript, closedOtuTables.head, closedOtuTable))
+ }
+
+ //TODO: Plots
+
+ }
}
/**
@@ -45,11 +76,6 @@ class Gears(val root: Configurable) extends QScript with MultiSampleQScript { qs
def makeSample(id: String): Sample = new Sample(id)
class Sample(sampleId: String) extends AbstractSample(sampleId) {
- /** Function to add sample jobs */
- protected def addJobs(): Unit = {
- addPerLibJobs()
- }
-
/**
* Factory method for Library class
* @param id SampleId
@@ -83,6 +109,40 @@ class Gears(val root: Configurable) extends QScript with MultiSampleQScript { qs
def summaryStats = Map()
}
+ private var _closedOtuTable: Option[File] = _
+ def closedOtuTable = _closedOtuTable
+
+ private var _closedOtuMap: Option[File] = _
+ def closedOtuMap = _closedOtuMap
+
+ /** Function to add sample jobs */
+ protected def addJobs(): Unit = {
+ addPerLibJobs()
+ val qiimeClosed = libraries.values.flatMap(_.gs.qiimeClosed).toList
+ if (qiimeClosed.nonEmpty) {
+ _closedOtuTable = Some(new File(sampleDir, "closed.biom"))
+ _closedOtuMap = Some(new File(sampleDir, "closed.map.txt"))
+ if (qiimeClosed.size > 1) {
+ val mergeTables = new MergeOtuTables(qscript)
+ mergeTables.input = qiimeClosed.map(_.otuTable).toList
+ mergeTables.outputFile = _closedOtuTable.get
+ add(mergeTables)
+
+ val mergeMaps = new MergeOtuTables(qscript)
+ mergeMaps.input = qiimeClosed.map(_.otuMap).toList
+ mergeMaps.outputFile = _closedOtuMap.get
+ add(mergeMaps)
+
+ } else {
+ add(Ln(qscript, qiimeClosed.head.otuMap, _closedOtuMap.get))
+ add(Ln(qscript, qiimeClosed.head.otuTable, _closedOtuTable.get))
+ }
+ } else {
+ _closedOtuTable = None
+ _closedOtuMap = None
+ }
+ }
+
/** Must return files to store into summary */
def summaryFiles: Map[String, File] = Map()
--
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