Commit 8a617e00 authored by Wai Yi Leung's avatar Wai Yi Leung
Browse files

Merge branch 'hotfix-v0.3.1'

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