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Commit 8a617e00 authored by Wai Yi Leung's avatar Wai Yi Leung
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Merge branch 'hotfix-v0.3.1'

parents b0774761 d2efef6d
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pom.xml
View file @ 8a617e00
......@@ -9,7 +9,7 @@
<parent>
<groupId>nl.lumc.sasc</groupId>
<artifactId>Biopet</artifactId>
<version>0.3.0</version>
<version>0.3.1</version>
<relativePath>public</relativePath>
</parent>
......
protected/biopet-gatk-extensions/pom.xml
View file @ 8a617e00
......@@ -16,7 +16,7 @@
<parent>
<groupId>nl.lumc.sasc</groupId>
<artifactId>BiopetGatk</artifactId>
<version>0.3.0</version>
<version>0.3.1</version>
<relativePath>../</relativePath>
</parent>
......
protected/biopet-gatk-pipelines/pom.xml
View file @ 8a617e00
......@@ -16,7 +16,7 @@
<parent>
<groupId>nl.lumc.sasc</groupId>
<artifactId>BiopetGatk</artifactId>
<version>0.3.0</version>
<version>0.3.1</version>
<relativePath>../</relativePath>
</parent>
......
protected/biopet-protected-package/pom.xml
View file @ 8a617e00
......@@ -16,7 +16,7 @@
<parent>
<groupId>nl.lumc.sasc</groupId>
<artifactId>BiopetGatk</artifactId>
<version>0.3.0</version>
<version>0.3.1</version>
<relativePath>../</relativePath>
</parent>
......
protected/pom.xml
View file @ 8a617e00
......@@ -11,7 +11,7 @@
<parent>
<groupId>nl.lumc.sasc</groupId>
<artifactId>BiopetRoot</artifactId>
<version>0.3.0</version>
<version>0.3.1</version>
<relativePath>../</relativePath>
</parent>
<artifactId>BiopetGatk</artifactId>
......
public/bam2wig/pom.xml
View file @ 8a617e00
......@@ -28,7 +28,7 @@
<parent>
<groupId>nl.lumc.sasc</groupId>
<artifactId>Biopet</artifactId>
<version>0.3.0</version>
<version>0.3.1</version>
<relativePath>../</relativePath>
</parent>
......
public/bammetrics/pom.xml
View file @ 8a617e00
......@@ -26,7 +26,7 @@
<parent>
<groupId>nl.lumc.sasc</groupId>
<artifactId>Biopet</artifactId>
<version>0.3.0</version>
<version>0.3.1</version>
<relativePath>../</relativePath>
</parent>
......
public/basty/pom.xml
View file @ 8a617e00
......@@ -33,7 +33,7 @@
<parent>
<groupId>nl.lumc.sasc</groupId>
<artifactId>Biopet</artifactId>
<version>0.3.0</version>
<version>0.3.1</version>
<relativePath>../</relativePath>
</parent>
......
public/biopet-framework/pom.xml
View file @ 8a617e00
......@@ -26,7 +26,7 @@
<parent>
<groupId>nl.lumc.sasc</groupId>
<artifactId>Biopet</artifactId>
<version>0.3.0</version>
<version>0.3.1</version>
<relativePath>../</relativePath>
</parent>
......
public/biopet-public-package/pom.xml
View file @ 8a617e00
......@@ -26,7 +26,7 @@
<parent>
<groupId>nl.lumc.sasc</groupId>
<artifactId>Biopet</artifactId>
<version>0.3.0</version>
<version>0.3.1</version>
<relativePath>../</relativePath>
</parent>
......
public/carp/pom.xml
View file @ 8a617e00
......@@ -26,7 +26,7 @@
<parent>
<groupId>nl.lumc.sasc</groupId>
<artifactId>Biopet</artifactId>
<version>0.3.0</version>
<version>0.3.1</version>
<relativePath>../</relativePath>
</parent>
......
public/flexiprep/pom.xml
View file @ 8a617e00
......@@ -26,7 +26,7 @@
<parent>
<groupId>nl.lumc.sasc</groupId>
<artifactId>Biopet</artifactId>
<version>0.3.0</version>
<version>0.3.1</version>
<relativePath>../</relativePath>
</parent>
......
public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
View file @ 8a617e00
......@@ -166,14 +166,16 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
var R1: File = new File(R1_in)
var R2: File = if (paired) new File(R2_in) else null
var deps: List[File] = if (paired) List(R1, R2) else List(R1)
var deps_R1: List[File] = R1 :: Nil
var deps_R2: List[File] = if (paired) R2 :: Nil else Nil
def deps: List[File] = deps_R1 ::: deps_R2
val seqtkSeq_R1 = SeqtkSeq(this, R1, swapExt(outDir, R1, R1_ext, ".sanger" + R1_ext), fastqc_R1)
seqtkSeq_R1.isIntermediate = true
add(seqtkSeq_R1)
addSummarizable(seqtkSeq_R1, "seqtkSeq_R1")
R1 = seqtkSeq_R1.output
deps ::= R1
deps_R1 ::= R1
if (paired) {
val seqtkSeq_R2 = SeqtkSeq(this, R2, swapExt(outDir, R2, R2_ext, ".sanger" + R2_ext), fastqc_R2)
......@@ -181,17 +183,19 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
add(seqtkSeq_R2)
addSummarizable(seqtkSeq_R2, "seqtkSeq_R2")
R2 = seqtkSeq_R2.output
deps ::= R2
deps_R2 ::= R2
}
val seqstat_R1 = Seqstat(this, R1, outDir)
seqstat_R1.isIntermediate = true
seqstat_R1.deps = deps_R1
add(seqstat_R1)
addSummarizable(seqstat_R1, "seqstat_R1")
if (paired) {
val seqstat_R2 = Seqstat(this, R2, outDir)
seqstat_R2.isIntermediate = true
seqstat_R2.deps = deps_R2
add(seqstat_R2)
addSummarizable(seqstat_R2, "seqstat_R2")
}
......@@ -201,10 +205,11 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
val cutadapt_R1 = Cutadapt(this, R1, swapExt(outDir, R1, R1_ext, ".clip" + R1_ext))
cutadapt_R1.fastqc = fastqc_R1
cutadapt_R1.isIntermediate = true
cutadapt_R1.deps = deps_R1
add(cutadapt_R1)
addSummarizable(cutadapt_R1, "clipping_R1")
R1 = cutadapt_R1.fastq_output
deps ::= R1
deps_R1 ::= R1
outputFiles += ("cutadapt_R1_stats" -> cutadapt_R1.stats_output)
if (paired) {
......@@ -212,10 +217,11 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
outputFiles += ("cutadapt_R2_stats" -> cutadapt_R2.stats_output)
cutadapt_R2.fastqc = fastqc_R2
cutadapt_R2.isIntermediate = true
cutadapt_R2.deps = deps_R2
add(cutadapt_R2)
addSummarizable(cutadapt_R2, "clipping_R2")
R2 = cutadapt_R2.fastq_output
deps ::= R2
deps_R2 ::= R2
val fqSync = new FastqSync(this)
fqSync.refFastq = cutadapt_R1.fastq_input
......@@ -230,7 +236,8 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
outputFiles += ("syncStats" -> fqSync.outputStats)
R1 = fqSync.outputFastq1
R2 = fqSync.outputFastq2
deps :::= R1 :: R2 :: Nil
deps_R1 ::= R1
deps_R2 ::= R2
}
}
......@@ -253,13 +260,13 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
}
val seqstat_R1_after = Seqstat(this, R1, outDir)
seqstat_R1_after.deps = deps
seqstat_R1_after.deps = deps_R1
add(seqstat_R1_after)
addSummarizable(seqstat_R1_after, "seqstat_R1_after")
if (paired) {
val seqstat_R2_after = Seqstat(this, R2, outDir)
seqstat_R2_after.deps = deps
seqstat_R2_after.deps = deps_R2
add(seqstat_R2_after)
addSummarizable(seqstat_R2_after, "seqstat_R2_after")
}
......
public/gentrap/pom.xml
View file @ 8a617e00
......@@ -26,7 +26,7 @@
<parent>
<groupId>nl.lumc.sasc</groupId>
<artifactId>Biopet</artifactId>
<version>0.3.0</version>
<version>0.3.1</version>
<relativePath>../</relativePath>
</parent>
......
public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/extensions/CustomVarScan.scala
View file @ 8a617e00
......@@ -63,20 +63,27 @@ class CustomVarScan(val root: Configurable) extends BiopetCommandLineFunction {
override def cmdLine: String = required(executable) + required("-vP") + required("""\t\t""")
}
private def varscan = new Mpileup2cns(wrapper.root) {
private val varscan = new Mpileup2cns(wrapper.root) {
strandFilter = Option(0)
outputVcf = Option(1)
}
private def compress = new Bgzip(wrapper.root) {
this.output = wrapper.output
}
private val compress = new Bgzip(wrapper.root)
private def index = new Tabix(wrapper.root) {
private val index = new Tabix(wrapper.root) {
input = compress.output
p = Option("vcf")
}
override def freezeFieldValues(): Unit = {
varscan.output = Option(new File(wrapper.output.toString.stripSuffix(".gz")))
compress.input = List(varscan.output.get)
compress.output = this.output
super.freezeFieldValues()
varscan.qSettings = this.qSettings
varscan.freezeFieldValues()
}
override def beforeGraph: Unit = {
require(output.toString.endsWith(".gz"), "Output must have a .gz file extension")
}
......@@ -85,6 +92,6 @@ class CustomVarScan(val root: Configurable) extends BiopetCommandLineFunction {
// FIXME: manual trigger of commandLine for version retrieval
mpileup.commandLine
mpileup.cmdPipe + " | " + fixMpileup.commandLine + " | " + removeEmptyPile.commandLine + " | " +
varscan.commandLine + " | " + compress.commandLine + " && " + index.commandLine
varscan.commandLine + " && " + compress.commandLine + " && " + index.commandLine
}
}
public/kopisu/pom.xml
View file @ 8a617e00
......@@ -26,7 +26,7 @@
<parent>
<groupId>nl.lumc.sasc</groupId>
<artifactId>Biopet</artifactId>
<version>0.3.0</version>
<version>0.3.1</version>
<relativePath>../</relativePath>
</parent>
......
public/mapping/pom.xml
View file @ 8a617e00
......@@ -26,7 +26,7 @@
<parent>
<groupId>nl.lumc.sasc</groupId>
<artifactId>Biopet</artifactId>
<version>0.3.0</version>
<version>0.3.1</version>
<relativePath>../</relativePath>
</parent>
......
public/pom.xml
View file @ 8a617e00
......@@ -22,7 +22,7 @@
<groupId>nl.lumc.sasc</groupId>
<name>Biopet</name>
<packaging>pom</packaging>
<version>0.3.0</version>
<version>0.3.1</version>
<modules>
<module>biopet-framework</module>
......
public/sage/pom.xml
View file @ 8a617e00
......@@ -26,7 +26,7 @@
<parent>
<groupId>nl.lumc.sasc</groupId>
<artifactId>Biopet</artifactId>
<version>0.3.0</version>
<version>0.3.1</version>
<relativePath>../</relativePath>
</parent>
......
public/shiva/pom.xml
View file @ 8a617e00
......@@ -22,7 +22,7 @@
<parent>
<artifactId>Biopet</artifactId>
<groupId>nl.lumc.sasc</groupId>
<version>0.3.0</version>
<version>0.3.1</version>
</parent>
<modelVersion>4.0.0</modelVersion>
......
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