From 5448ee5880e98f93ff5e2feac8025e65fab37153 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 27 Oct 2015 15:19:42 +0100
Subject: [PATCH] Added input files to summary of shiva
---
.../biopet/pipelines/shiva/ShivaTrait.scala | 30 +++++++++++--------
1 file changed, 18 insertions(+), 12 deletions(-)
diff --git a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala
index 8a0cdb439..c51eb6331 100644
--- a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala
+++ b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala
@@ -91,11 +91,13 @@ trait ShivaTrait extends MultiSampleQScript with Reference {
class Library(libId: String) extends AbstractLibrary(libId) {
/** Library specific files to add to the summary */
def summaryFiles: Map[String, File] = {
- (bamFile, preProcessBam) match {
+ ((bamFile, preProcessBam) match {
case (Some(b), Some(pb)) => Map("bamFile" -> b, "preProcessBam" -> pb)
case (Some(b), _) => Map("bamFile" -> b)
case _ => Map()
- }
+ }) ++ (inputR1.map("input_R1" -> _) ::
+ inputR2.map("input_R2" -> _) ::
+ inputBam.map("input_bam" -> _) :: Nil).flatten.toMap
}
/** Library specific stats to add to summary */
@@ -117,8 +119,12 @@ trait ShivaTrait extends MultiSampleQScript with Reference {
(Some(mapping), Some(mapping.finalBamFile), preProcess(mapping.finalBamFile))
}
+ lazy val inputR1: Option[File] = config("R1")
+ lazy val inputR2: Option[File] = config("R2")
+ lazy val inputBam: Option[File] = if (r1.isEmpty) config("bam") else None
+
lazy val (mapping, bamFile, preProcessBam): (Option[Mapping], Option[File], Option[File]) =
- (config.contains("R1"), config.contains("bam")) match {
+ (inputR1.isDefined, inputBam.isDefined) match {
case (true, _) => makeMapping // Default starting from fastq files
case (false, true) => // Starting from bam file
config("bam_to_fastq", default = false).asBoolean match {
@@ -137,18 +143,18 @@ trait ShivaTrait extends MultiSampleQScript with Reference {
/** This will add jobs for this library */
def addJobs(): Unit = {
- (config.contains("R1"), config.contains("bam")) match {
+ (inputR1.isDefined, inputBam.isDefined) match {
case (true, _) => mapping.foreach(mapping => {
- mapping.input_R1 = config("R1")
- mapping.input_R2 = config("R2")
+ mapping.input_R1 = inputR1.get
+ mapping.input_R2 = inputR2
inputFiles :+= new InputFile(mapping.input_R1, config("R1_md5"))
mapping.input_R2.foreach(inputFiles :+= new InputFile(_, config("R2_md5")))
})
case (false, true) => {
- inputFiles :+= new InputFile(config("bam"), config("bam_md5"))
+ inputFiles :+= new InputFile(inputBam.get, config("bam_md5"))
config("bam_to_fastq", default = false).asBoolean match {
case true =>
- val samToFastq = SamToFastq(qscript, config("bam"),
+ val samToFastq = SamToFastq(qscript, inputBam.get,
new File(libDir, sampleId + "-" + libId + ".R1.fq.gz"),
new File(libDir, sampleId + "-" + libId + ".R2.fq.gz"))
samToFastq.isIntermediate = true
@@ -158,7 +164,7 @@ trait ShivaTrait extends MultiSampleQScript with Reference {
mapping.input_R2 = Some(samToFastq.fastqR2)
})
case false =>
- val inputSam = SamReaderFactory.makeDefault.open(config("bam"))
+ val inputSam = SamReaderFactory.makeDefault.open(inputBam.get)
val readGroups = inputSam.getFileHeader.getReadGroups
val readGroupOke = readGroups.forall(readGroup => {
@@ -170,8 +176,8 @@ trait ShivaTrait extends MultiSampleQScript with Reference {
if (!readGroupOke) {
if (config("correct_readgroups", default = false).asBoolean) {
- logger.info("Correcting readgroups, file:" + config("bam"))
- val aorrg = AddOrReplaceReadGroups(qscript, config("bam"), bamFile.get)
+ logger.info("Correcting readgroups, file:" + inputBam.get)
+ val aorrg = AddOrReplaceReadGroups(qscript, inputBam.get, bamFile.get)
aorrg.RGID = sampleId + "-" + libId
aorrg.RGLB = libId
aorrg.RGSM = sampleId
@@ -180,7 +186,7 @@ trait ShivaTrait extends MultiSampleQScript with Reference {
} else throw new IllegalStateException("Sample readgroup and/or library of input bamfile is not correct, file: " + bamFile +
"\nPlease note that it is possible to set 'correct_readgroups' to true in the config to automatic fix this")
} else {
- val oldBamFile: File = config("bam")
+ val oldBamFile: File = inputBam.get
val oldIndex: File = new File(oldBamFile.getAbsolutePath.stripSuffix(".bam") + ".bai")
val newIndex: File = new File(libDir, oldBamFile.getName.stripSuffix(".bam") + ".bai")
val baiLn = Ln(qscript, oldIndex, newIndex)
--
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