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 876fa8cacb6c4b29e4547e0f72cac27ff1f551e8..ee75d08759a85e88dc5cbe5297048518a869aeb4 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
@@ -86,20 +86,18 @@ class Flexiprep(private var globalConfig: Config) extends QScript with BiopetQSc
}
def getQualtype(fastqc:Fastqc, pairname:String): File = {
- val fastqcToQualtype = new FastqcToQualtype(config) {
- this.fastqc_output = fastqc.output
- this.out = new File(outputDir + pairname + ".qualtype.txt")
- }
+ val fastqcToQualtype = new FastqcToQualtype(config)
+ fastqcToQualtype.fastqc_output = fastqc.output
+ fastqcToQualtype.out = new File(outputDir + pairname + ".qualtype.txt")
add(fastqcToQualtype)
return fastqcToQualtype.out
}
def getContams(fastqc:Fastqc, pairname:String): File = {
- val fastqcToContams = new FastqcToContams(config) {
- this.fastqc_output = fastqc.output
- this.out = new File(outputDir + pairname + ".contams.txt")
- this.contams_file = fastqc.contaminants
- }
+ val fastqcToContams = new FastqcToContams(config)
+ fastqcToContams.fastqc_output = fastqc.output
+ fastqcToContams.out = new File(outputDir + pairname + ".contams.txt")
+ fastqcToContams.contams_file = fastqc.contaminants
add(fastqcToContams)
return fastqcToContams.out
}
@@ -120,32 +118,29 @@ class Flexiprep(private var globalConfig: Config) extends QScript with BiopetQSc
var R2: File = new File(R2_in)
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")
- }
+ val cutadapt_R1 = new Cutadapt(config)
+ if (!skipTrim || paired) cutadapt_R1.isIntermediate = true
+ cutadapt_R1.fastq_input = R1
+ cutadapt_R1.fastq_output = swapExt(outDir, R1, R1_ext, ".clip"+R1_ext)
+ if (outputFiles.contains("contams_R1")) cutadapt_R1.contams_file = outputFiles("contams_R1")
add(cutadapt_R1)
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")
- }
+ val cutadapt_R2 = new Cutadapt(config)
+ if (!skipTrim || paired) cutadapt_R2.isIntermediate = true
+ cutadapt_R2.fastq_input = R2
+ cutadapt_R2.fastq_output = swapExt(outDir, R2, R2_ext, ".clip"+R2_ext)
+ if (outputFiles.contains("contams_R2")) cutadapt_R2.contams_file = outputFiles("contams_R2")
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
- this.output_R1 = swapExt(outDir, R1, R1_ext, ".sync"+R1_ext)
- this.output_R2 = swapExt(outDir, R2, R2_ext, ".sync"+R2_ext)
- this.output_stats = swapExt(outDir, R1, R1_ext, ".sync.stats")
- }
+ val fastqSync = new FastqSync(config)
+ if (!skipTrim) fastqSync.isIntermediate = true
+ fastqSync.input_start_fastq = cutadapt_R1.fastq_input
+ fastqSync.input_R1 = cutadapt_R1.fastq_output
+ fastqSync.input_R2 = cutadapt_R2.fastq_output
+ fastqSync.output_R1 = swapExt(outDir, R1, R1_ext, ".sync"+R1_ext)
+ fastqSync.output_R2 = swapExt(outDir, R2, R2_ext, ".sync"+R2_ext)
+ fastqSync.output_stats = swapExt(outDir, R1, R1_ext, ".sync.stats")
add(fastqSync)
outputFiles += ("syncStats" -> fastqSync.output_stats)
R1 = fastqSync.output_R1
@@ -154,19 +149,18 @@ class Flexiprep(private var globalConfig: Config) extends QScript with BiopetQSc
}
if (!skipTrim) { // Quality trimming
- val sickle = new Sickle(config) {
- 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")
+ val sickle = new Sickle(config)
+ sickle.input_R1 = 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 :+= outputFiles(chunk + "fastq_input_R1")
+ if (paired) {
+ 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)
+ if (!skipClip) sickle.deps :+= outputFiles(chunk + "fastq_input_R2")
}
+ sickle.output_stats = swapExt(outDir, R1, R1_ext, ".trim.stats")
add(sickle)
R1 = sickle.output_R1
if (paired) R2 = sickle.output_R2
@@ -213,15 +207,14 @@ class Flexiprep(private var globalConfig: Config) extends QScript with BiopetQSc
if (paired) outputFiles += ("fastqc_R2_final" -> runFastqc(outputFiles("output_R2"),outputDir + "/" + R2_name + ".qc.fastqc/").output)
}
- val summarize = new Summarize(config) {
- this.runDir = outputDir
- this.samplea = R1_name
- if (paired) this.sampleb = R2_name
- this.samplename = R1_name
- this.clip = !skipClip
- this.trim = !skipTrim
- this.out = new File(outputDir + R1_name + ".summary.json")
- }
+ val summarize = new Summarize(config)
+ summarize.runDir = outputDir
+ summarize.samplea = R1_name
+ if (paired) summarize.sampleb = R2_name
+ summarize.samplename = R1_name
+ summarize.clip = !skipClip
+ summarize.trim = !skipTrim
+ summarize.out = new File(outputDir + R1_name + ".summary.json")
for ((k,v) <- outputFiles) summarize.deps +:= v
add(summarize)
}
@@ -235,6 +228,7 @@ class Flexiprep(private var globalConfig: Config) extends QScript with BiopetQSc
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.ouput"
+ fastqcCommand.afterGraph
add(fastqcCommand)
return fastqcCommand
}
@@ -244,18 +238,19 @@ class Flexiprep(private var globalConfig: Config) extends QScript with BiopetQSc
var newFile: File = swapExt(file,".gz","")
if (file.getName().endsWith(".gzip")) newFile = swapExt(file,".gzip","")
val zcatCommand = new Zcat(config)
- zcatCommand.in = file
- zcatCommand.out = new File(runDir + newFile)
+ zcatCommand.input = file
+ zcatCommand.output = new File(runDir + newFile)
//zcatCommand.jobOutputFile = outputDir + "." + file.getName + ".out"
if (!this.skipClip || !this.skipTrim) zcatCommand.isIntermediate = true
add(zcatCommand)
- return zcatCommand.out
+ return zcatCommand.output
} else return file
}
def addSeqstat(fastq:File, key:String) {
val ext = fastq.getName.substring(fastq.getName.lastIndexOf("."))
- val seqstat = new Seqstat(config) { this.input_fastq = fastq }
+ val seqstat = new Seqstat(config)
+ seqstat.input_fastq = fastq
seqstat.out = swapExt(outputDir, fastq, ext, ".seqstats.json")
add(seqstat)
outputFiles += (key -> seqstat.out)
@@ -263,10 +258,11 @@ class Flexiprep(private var globalConfig: Config) extends QScript with BiopetQSc
def addSha1sum(fastq:File, key:String) {
val ext = fastq.getName.substring(fastq.getName.lastIndexOf("."))
- val sha1sum = new Sha1sum(config) { this.in = fastq }
- sha1sum.out = swapExt(outputDir, fastq, ext, ".sha1")
+ val sha1sum = new Sha1sum(config)
+ sha1sum.input = fastq
+ sha1sum.output = swapExt(outputDir, fastq, ext, ".sha1")
add(sha1sum)
- outputFiles += (key -> sha1sum.out)
+ outputFiles += (key -> sha1sum.output)
}
}
diff --git a/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala b/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
index d8174acac9a0fb925a85ce9543022d373d37b409..a2d2c8ce704722fa8828c0ec89745424788ad8ec 100644
--- a/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
+++ b/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
@@ -83,25 +83,33 @@ class Mapping(private var globalConfig: Config) extends QScript with BiopetQScri
}
var bamFile:File = null
if (aligner == "bwa") {
- val bwaCommand = new Bwa(config) { R1 = fastq_R1; if (paired) R2 = fastq_R2;
- RG = getReadGroup; output = new File(outputDir + outputName + ".sam") }
+ val bwaCommand = new Bwa(config)
+ bwaCommand.R1 = fastq_R1
+ if (paired) bwaCommand.R2 = fastq_R2
+ bwaCommand.RG = getReadGroup
+ bwaCommand.output = new File(outputDir + outputName + ".sam")
add(bwaCommand)
bamFile = addSortSam(List(bwaCommand.output), swapExt(outputDir,bwaCommand.output,".sam",".bam"), outputDir)
} else if (aligner == "star") {
- val starCommand = new Star(config) { R1 = fastq_R1; if (paired) R2 = fastq_R2; this.outputDir = qscript.outputDir + "star/"; init}
+ val starCommand = Star(config, fastq_R1, if (paired) fastq_R2 else null, outputDir)
add(starCommand)
bamFile = addAddOrReplaceReadGroups(List(starCommand.outputSam), new File(outputDir + outputName + ".bam"), outputDir)
} else if (aligner == "star-2pass") {
- val starCommand_pass1 = new Star(config) { R1 = fastq_R1; if (paired) R2 = fastq_R2;
- this.outputDir = qscript.outputDir + "star-2pass/aln-pass1/"; init}
+ val starCommand_pass1 = Star(config, fastq_R1, if (paired) fastq_R2 else null, outputDir + "star-2pass/aln-pass1/")
+ starCommand_pass1.afterGraph
add(starCommand_pass1)
- val starCommand_reindex = new Star(config) { this.sjdbFileChrStartEnd = starCommand_pass1.outputTab;
- this.outputDir = qscript.outputDir + "star-2pass/re-index/" ; this.runmode = "genomeGenerate"; this.sjdbOverhang = 75; init}
+ val starCommand_reindex = new Star(config)
+ starCommand_reindex.sjdbFileChrStartEnd = starCommand_pass1.outputTab
+ starCommand_reindex.outputDir = qscript.outputDir + "star-2pass/re-index/"
+ starCommand_reindex.runmode = "genomeGenerate"
+ starCommand_reindex.sjdbOverhang = 75
+ starCommand_reindex.afterGraph
add(starCommand_reindex)
- val starCommand_pass2 = new Star(config) { R1 = fastq_R1; if (paired) R2 = fastq_R2; this.deps ++= starCommand_reindex.outputs;
- this.outputDir = qscript.outputDir + "star-2pass/aln-pass2/"; this.genomeDir = starCommand_reindex.outputDir; init}
+ val starCommand_pass2 = Star(config, fastq_R1, if (paired) fastq_R2 else null, outputDir + "star-2pass/aln-pass2/")
+ starCommand_pass2.genomeDir = starCommand_reindex.outputDir
+ starCommand_pass2.afterGraph
add(starCommand_pass2)
bamFile = addAddOrReplaceReadGroups(List(starCommand_pass2.outputSam), new File(outputDir + outputName + ".bam"), outputDir)
} else throw new IllegalStateException("Option Alginer: '" + aligner + "' is not valid")