From 991903f55acf74199a2e76eae25b4f6ed0ee5593 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Wed, 4 Jun 2014 14:50:52 +0200
Subject: [PATCH] Marked temp files as intermediate
---
.../pipelines/flexiprep/Flexiprep.scala | 49 +++++++++++--------
1 file changed, 28 insertions(+), 21 deletions(-)
diff --git a/flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala b/flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
index 1a0173d49..a06465661 100644
--- a/flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
+++ b/flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
@@ -56,24 +56,18 @@ class Flexiprep(private var globalConfig: Config) extends QScript with BiopetQSc
init()
runInitialFastqc()
- outputFiles += ("output_R1" -> zcatIfNeeded(input_R1,outputDir))
- if (paired) outputFiles += ("output_R2" -> zcatIfNeeded(input_R2,outputDir))
+ outputFiles += ("fastq_input_R1" -> zcatIfNeeded(input_R1,outputDir))
+ if (paired) outputFiles += ("fastq_input_R2" -> zcatIfNeeded(input_R2,outputDir))
- addSeqstat(outputFiles("output_R1"), "seqstat_R1")
- if (paired) addSeqstat(outputFiles("output_R2"), "seqstat_qc_R2")
+ addSeqstat(outputFiles("fastq_input_R1"), "seqstat_R1")
+ if (paired) addSeqstat(outputFiles("fastq_input_R2"), "seqstat_R2")
- addSha1sum(outputFiles("output_R1"), "sha1_R1")
- if (paired) addSha1sum(outputFiles("output_R2"), "sha1_R2")
+ addSha1sum(outputFiles("fastq_input_R1"), "sha1_R1")
+ if (paired) addSha1sum(outputFiles("fastq_input_R2"), "sha1_R2")
+
+ if (paired) runTrimClip(outputFiles("fastq_input_R1"), outputFiles("fastq_input_R2"), outputDir)
+ else runTrimClip(outputFiles("fastq_input_R1"), outputDir)
- var results: Map[String,File] = Map()
- if (paired) {
- results = runTrimClip(outputFiles("output_R1"), outputFiles("output_R2"), outputDir)
- outputFiles += ("output_R1" -> results("output_R1"))
- outputFiles += ("output_R2" -> results("output_R2"))
- } else {
- results = runTrimClip(outputFiles("output_R1"), outputDir)
- outputFiles += ("output_R1" -> results("output_R1"))
- }
runFinalize(List(outputFiles("output_R1")), List(outputFiles("output_R2")))
}
@@ -110,10 +104,16 @@ class Flexiprep(private var globalConfig: Config) extends QScript with BiopetQSc
return fastqcToContams.out
}
- def runTrimClip(R1_in:File, outDir:String) : Map[String,File] = {
- return runTrimClip(R1_in, new File(""), outDir)
+ def runTrimClip(R1_in:File, outDir:String, chunk:String) {
+ runTrimClip(R1_in, new File(""), outDir, chunk)
+ }
+ def runTrimClip(R1_in:File, outDir:String) {
+ runTrimClip(R1_in, new File(""), outDir, "")
+ }
+ def runTrimClip(R1_in:File, R2_in:File, outDir:String) {
+ runTrimClip(R1_in, R2_in, outDir, "")
}
- def runTrimClip(R1_in:File, R2_in:File, outDir:String) : Map[String,File] = {
+ def runTrimClip(R1_in:File, R2_in:File, outDir:String, chunk:String) {
var results: Map[String,File] = Map()
var R1: File = new File(R1_in)
@@ -121,6 +121,7 @@ class Flexiprep(private var globalConfig: Config) extends QScript with BiopetQSc
if (!skipClip) { // Adapter clipping
val cutadapt_R1 = new Cutadapt(config) {
+ if (!skipTrim || paired) this.isIntermediate = true
this.fastq_input = R1
this.fastq_output = swapExt(outDir, R1, R1_ext, ".clip"+R1_ext)
if (outputFiles.contains("contams_R1")) this.contams_file = outputFiles("contams_R1")
@@ -129,6 +130,7 @@ class Flexiprep(private var globalConfig: Config) extends QScript with BiopetQSc
R1 = cutadapt_R1.fastq_output
if (paired) {
val cutadapt_R2 = new Cutadapt(config) {
+ if (!skipTrim || paired) this.isIntermediate = true
this.fastq_input = R2
this.fastq_output = swapExt(outDir, R2, R2_ext, ".clip"+R2_ext)
if (outputFiles.contains("contams_R2")) this.contams_file = outputFiles("contams_R2")
@@ -136,6 +138,7 @@ class Flexiprep(private var globalConfig: Config) extends QScript with BiopetQSc
add(cutadapt_R2)
R2 = cutadapt_R2.fastq_output
val fastqSync = new FastqSync(config) {
+ if (!skipTrim) this.isIntermediate = true
this.input_start_fastq = cutadapt_R1.fastq_input
this.input_R1 = cutadapt_R1.fastq_output
this.input_R2 = cutadapt_R2.fastq_output
@@ -144,6 +147,7 @@ class Flexiprep(private var globalConfig: Config) extends QScript with BiopetQSc
this.output_stats = swapExt(outDir, R1, R1_ext, ".sync.stats")
}
add(fastqSync)
+ outputFiles += ("syncStats" -> fastqSync.output_stats)
R1 = fastqSync.output_R1
R2 = fastqSync.output_R2
}
@@ -154,10 +158,12 @@ class Flexiprep(private var globalConfig: Config) extends QScript with BiopetQSc
this.input_R1 = R1
this.output_R1 = swapExt(outDir, R1, R1_ext, ".trim"+R1_ext)
if (outputFiles.contains("qualtype_R1")) this.qualityTypeFile = outputFiles("qualtype_R1")
+ if (!skipClip) this.deps :+= outputFiles(chunk + "fastq_input_R1")
if (paired) {
this.input_R2 = R2
this.output_R2 = swapExt(outDir, R2, R2_ext, ".trim"+R2_ext)
this.output_singles = swapExt(outDir, R2, R2_ext, ".trim.singles"+R1_ext)
+ if (!skipClip) this.deps :+= outputFiles(chunk + "fastq_input_R2")
}
this.output_stats = swapExt(outDir, R1, R1_ext, ".trim.stats")
}
@@ -166,9 +172,8 @@ class Flexiprep(private var globalConfig: Config) extends QScript with BiopetQSc
if (paired) R2 = sickle.output_R2
}
- results += ("output_R1" -> R1)
- if (paired) results += ("output_R2" -> R2)
- return results
+ outputFiles += ("output_R1" -> R1)
+ if (paired) outputFiles += ("output_R2" -> R2)
}
def runFinalize(fastq_R1:List[File], fastq_R2:List[File]) {
@@ -239,6 +244,8 @@ class Flexiprep(private var globalConfig: Config) extends QScript with BiopetQSc
val zcatCommand = new Zcat(config)
zcatCommand.in = file
zcatCommand.out = new File(runDir + newFile)
+ //zcatCommand.jobOutputFile = outputDir + "." + file.getName + ".out"
+ if (!this.skipClip || !this.skipTrim) zcatCommand.isIntermediate = true
add(zcatCommand)
return zcatCommand.out
} else return file
--
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