From 16a08dfda02253c532f0707dd72ffc0b49ae02c1 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Sun, 27 Jul 2014 10:32:30 +0200
Subject: [PATCH] - Moved constructor to function itself - Add extract option
to fastqc
---
.../sasc/biopet/function/fastq/Fastqc.scala | 22 ++++++++++++++---
.../pipelines/flexiprep/Flexiprep.scala | 24 ++++---------------
2 files changed, 24 insertions(+), 22 deletions(-)
diff --git a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Fastqc.scala b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Fastqc.scala
index 413defa02..cc48a1682 100644
--- a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Fastqc.scala
+++ b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Fastqc.scala
@@ -18,13 +18,14 @@ class Fastqc(val root: Configurable) extends BiopetCommandLineFunction {
@Output(doc = "Output", shortName = "out")
var output: File = _
-
+
executable = config("exe", default = "fastqc")
var java_exe: String = config("exe", default = "java", submodule = "java")
var kmers: Option[Int] = config("kmers")
var quiet: Boolean = config("quiet")
var noextract: Boolean = config("noextract")
var nogroup: Boolean = config("nogroup")
+ var extract: Boolean = config("extract", default = true)
override val versionRegex = """FastQC (.*)""".r
override val defaultThreads = 4
@@ -45,9 +46,24 @@ class Fastqc(val root: Configurable) extends BiopetCommandLineFunction {
optional("--kmers", kmers) +
conditional(nogroup, "--nogroup") +
conditional(noextract, "--noextract") +
+ conditional(extract, "--extract") +
conditional(quiet, "--quiet") +
required("-o", output.getParent()) +
- required(fastqfile) +
- required(" > ", output, escape = false)
+ required(fastqfile)
}
}
+
+object Fastqc {
+ def apply(root:Configurable, fastqfile: File, outDir: String): Fastqc = {
+ val fastqcCommand = new Fastqc(root)
+ fastqcCommand.fastqfile = fastqfile
+ var filename: String = fastqfile.getName()
+ if (filename.endsWith(".gz")) filename = filename.substring(0, filename.size - 3)
+ if (filename.endsWith(".gzip")) filename = filename.substring(0, filename.size - 5)
+ if (filename.endsWith(".fastq")) filename = filename.substring(0, filename.size - 6)
+ //if (filename.endsWith(".fq")) filename = filename.substring(0,filename.size - 3)
+ fastqcCommand.jobOutputFile = new File(outDir + "/" + filename + "_fastqc.zip")
+ fastqcCommand.afterGraph
+ return fastqcCommand
+ }
+}
\ No newline at end of file
diff --git a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
index 38b9809da..00eb4cba9 100644
--- a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
+++ b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
@@ -81,13 +81,13 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
addSha1sum(outputFiles("fastq_input_R1"), "sha1_R1")
if (paired) addSha1sum(outputFiles("fastq_input_R2"), "sha1_R2")
- var fastqc_R1 = runFastqc(input_R1, outputDir + "/" + R1_name + ".fastqc/")
+ var fastqc_R1 = Fastqc(this, input_R1, outputDir + "/" + R1_name + ".fastqc/")
outputFiles += ("fastqc_R1" -> fastqc_R1.output)
outputFiles += ("qualtype_R1" -> getQualtype(fastqc_R1, R1_name))
outputFiles += ("contams_R1" -> getContams(fastqc_R1, R1_name))
if (paired) {
- var fastqc_R2 = runFastqc(input_R2, outputDir + "/" + R2_name + ".fastqc/")
+ var fastqc_R2 = Fastqc(this, input_R2, outputDir + "/" + R2_name + ".fastqc/")
outputFiles += ("fastqc_R2" -> fastqc_R2.output)
outputFiles += ("qualtype_R2" -> getQualtype(fastqc_R2, R2_name))
outputFiles += ("contams_R2" -> getContams(fastqc_R2, R2_name))
@@ -226,9 +226,9 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
addSha1sum(R1, "sha1_qc_R1")
if (paired) addSha1sum(R2, "sha1_qc_R2")
-
- outputFiles += ("fastqc_R1_final" -> runFastqc(outputFiles("output_R1"), outputDir + "/" + R1_name + ".qc.fastqc/").output)
- if (paired) outputFiles += ("fastqc_R2_final" -> runFastqc(outputFiles("output_R2"), outputDir + "/" + R2_name + ".qc.fastqc/").output)
+
+ outputFiles += ("fastqc_R1_final" -> Fastqc(this, outputFiles("output_R1"), outputDir + "/" + R1_name + ".qc.fastqc/").output)
+ if (paired) outputFiles += ("fastqc_R2_final" -> Fastqc(this, outputFiles("output_R2"), outputDir + "/" + R2_name + ".qc.fastqc/").output)
}
if (!skipSummary) {
@@ -245,20 +245,6 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
}
}
- def runFastqc(fastqfile: File, outDir: String): Fastqc = {
- val fastqcCommand = new Fastqc(this)
- fastqcCommand.fastqfile = fastqfile
- var filename: String = fastqfile.getName()
- if (filename.endsWith(".gz")) filename = filename.substring(0, filename.size - 3)
- if (filename.endsWith(".gzip")) filename = filename.substring(0, filename.size - 5)
- if (filename.endsWith(".fastq")) filename = filename.substring(0, filename.size - 6)
- //if (filename.endsWith(".fq")) filename = filename.substring(0,filename.size - 3)
- fastqcCommand.output = outDir + "/" + filename + "_fastqc.output"
- fastqcCommand.afterGraph
- add(fastqcCommand)
- return fastqcCommand
- }
-
def extractIfNeeded(file: File, runDir: String): File = {
if (file.getName().endsWith(".gz") || file.getName().endsWith(".gzip")) {
var newFile: File = swapExt(runDir, file, ".gz", "")
--
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