From 4818d27652c5c7bb941e5612652bc3d44bc41c29 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Sun, 15 May 2016 16:19:51 +0200
Subject: [PATCH] Added config for each genome
---
.../generateindexes/GenerateIndexes.scala | 21 ++++++++++++++-----
1 file changed, 16 insertions(+), 5 deletions(-)
diff --git a/generate-indexes/src/main/scala/nl/lumc/sasc/biopet/pipelines/generateindexes/GenerateIndexes.scala b/generate-indexes/src/main/scala/nl/lumc/sasc/biopet/pipelines/generateindexes/GenerateIndexes.scala
index a2c02fa8f..2fa39920c 100644
--- a/generate-indexes/src/main/scala/nl/lumc/sasc/biopet/pipelines/generateindexes/GenerateIndexes.scala
+++ b/generate-indexes/src/main/scala/nl/lumc/sasc/biopet/pipelines/generateindexes/GenerateIndexes.scala
@@ -42,9 +42,7 @@ class GenerateIndexes(val root: Configurable) extends QScript with BiopetQScript
var referenceConfig: Map[String, Any] = null
- var configDeps: List[File] = Nil
-
- def outputConfigFile = new File(outputDir, "reference.json")
+ protected var configDeps: List[File] = Nil
/** This is executed before the script starts */
def init(): Unit = {
@@ -59,6 +57,7 @@ class GenerateIndexes(val root: Configurable) extends QScript with BiopetQScript
val speciesConfig = ConfigUtils.any2map(c)
val speciesDir = new File(outputDir, speciesName)
for ((genomeName, c) <- speciesConfig) yield genomeName -> {
+ var configDeps: List[File] = Nil
val genomeConfig = ConfigUtils.any2map(c)
val fastaUris = genomeConfig.getOrElse("fasta_uri",
throw new IllegalArgumentException(s"No fasta_uri found for $speciesName - $genomeName")) match {
@@ -246,6 +245,18 @@ class GenerateIndexes(val root: Configurable) extends QScript with BiopetQScript
"bowtie_index" -> bowtie2Index.reference.getAbsolutePath.stripSuffix(".fa").stripSuffix(".fasta")
)
+ add(new InProcessFunction {
+ @Input val deps: List[File] = configDeps
+
+ @Output val out: File = new File(genomeDir, s"$speciesName-$genomeName.json")
+
+ def run: Unit = {
+ val writer = new PrintWriter(out)
+ writer.println(ConfigUtils.mapToJson(Map("references" -> Map(speciesName -> Map(genomeName -> outputConfig)))).spaces2)
+ writer.close()
+ }
+ })
+ this.configDeps :::= configDeps
outputConfig
}
}
@@ -253,10 +264,10 @@ class GenerateIndexes(val root: Configurable) extends QScript with BiopetQScript
add(new InProcessFunction {
@Input val deps: List[File] = configDeps
- @Output val out = outputConfigFile
+ @Output val out = new PrintWriter(outputDir, "references.json")
def run: Unit = {
- val writer = new PrintWriter(outputConfigFile)
+ val writer = new PrintWriter(out)
writer.println(ConfigUtils.mapToJson(Map("references" -> outputConfig)).spaces2)
writer.close()
}
--
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