Commit 2e45f064 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

intial unzipped file is intermediate now

parent 43881d8d
......@@ -143,6 +143,7 @@ class Flexiprep(val root:Configurable) extends QScript with BiopetQScript {
R2 = cutadapt_R2.fastq_output
val fastqSync = new FastqSync(this)
if (!skipTrim) fastqSync.isIntermediate = true
fastqSync.deps ++= Seq(outputFiles("fastq_input_R1"), outputFiles("fastq_input_R2"))
fastqSync.input_start_fastq = cutadapt_R1.fastq_input
fastqSync.input_R1 = cutadapt_R1.fastq_output
fastqSync.input_R2 = cutadapt_R2.fastq_output
......@@ -159,10 +160,12 @@ class Flexiprep(val root:Configurable) extends QScript with BiopetQScript {
if (!skipTrim) { // Quality trimming
val sickle = new Sickle(this)
sickle.input_R1 = R1
sickle.deps :+= outputFiles("fastq_input_R1")
sickle.output_R1 = swapExt(outDir, R1, R1_ext, ".trim"+R1_ext)
if (outputFiles.contains("qualtype_R1")) sickle.qualityTypeFile = outputFiles("qualtype_R1")
if (!skipClip) sickle.deps :+= R1_in
if (paired) {
sickle.deps :+= outputFiles("fastq_input_R2")
sickle.input_R2 = R2
sickle.output_R2 = swapExt(outDir, R2, R2_ext, ".trim"+R2_ext)
sickle.output_singles = swapExt(outDir, R2, R2_ext, ".trim.singles"+R1_ext)
......@@ -259,13 +262,13 @@ class Flexiprep(val root:Configurable) extends QScript with BiopetQScript {
var newFile: File = swapExt(runDir, file,".gz","")
if (file.getName().endsWith(".gzip")) newFile = swapExt(runDir, file,".gzip","")
val zcatCommand = Zcat(this, file, newFile)
if (!this.skipClip || !this.skipTrim) zcatCommand.isIntermediate = true
zcatCommand.isIntermediate = true
add(zcatCommand)
return newFile
} else if (file.getName().endsWith(".bz2")) {
var newFile = swapExt(runDir, file,".bz2","")
val pbzip2 = Pbzip2(this,file, newFile)
if (!this.skipClip || !this.skipTrim) pbzip2.isIntermediate = true
pbzip2.isIntermediate = true
add(pbzip2)
return newFile
} else return file
......
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