From 171522f4770ecf59321f4ab7864654639b973956 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 3 Jun 2014 11:47:16 +0200
Subject: [PATCH] Changed filenames for compatible summarize script
---
.../pipelines/flexiprep/Flexiprep.scala | 122 ++++++++++++++----
1 file changed, 97 insertions(+), 25 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 9ba56ea64..554101a2d 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
@@ -3,7 +3,6 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep
import nl.lumc.sasc.biopet.core._
import nl.lumc.sasc.biopet.wrappers._
import org.broadinstitute.sting.queue.QScript
-import org.broadinstitute.sting.queue.engine.JobRunInfo
import org.broadinstitute.sting.queue.extensions.gatk._
import org.broadinstitute.sting.queue.extensions.picard._
import org.broadinstitute.sting.queue.function._
@@ -21,8 +20,11 @@ class Flexiprep(private var globalConfig: Config) extends QScript with BiopetQSc
@Argument(doc="Skip Trim fastq files", shortName="skiptrim", required=false) var skipTrim: Boolean = false
@Argument(doc="Skip Clip fastq files", shortName="skipclip", required=false) var skipClip: Boolean = false
- //var outputFiles:Map[String,File] = Map()
var paired: Boolean = (input_R2 != null)
+ var R1_ext: String = _
+ var R2_ext: String = _
+ var R1_name: String = _
+ var R2_name: String = _
def init() {
for (file <- configfiles) globalConfig.loadConfigFile(file)
@@ -33,6 +35,20 @@ class Flexiprep(private var globalConfig: Config) extends QScript with BiopetQSc
if (outputDir == null) throw new IllegalStateException("Missing Output directory on flexiprep module")
else if (!outputDir.endsWith("/")) outputDir += "/"
paired = (input_R2 != null)
+
+ if (input_R1.endsWith(".gz")) R1_name = input_R1.getName.substring(0, input_R1.getName.lastIndexOf(".gz"))
+ else if (input_R1.endsWith(".gzip")) R1_name = input_R1.getName.substring(0, input_R1.getName.lastIndexOf(".gzip"))
+ else R1_name = input_R1
+ R1_ext = R1_name.substring(R1_name.lastIndexOf("."), R1_name.size)
+ R1_name = R1_name.substring(0, R1_name.lastIndexOf(R1_ext))
+
+ if (paired) {
+ if (input_R2.endsWith(".gz")) R2_name = input_R2.getName.substring(0, input_R2.getName.lastIndexOf(".gz"))
+ else if (input_R2.endsWith(".gzip")) R2_name = input_R2.getName.substring(0, input_R2.getName.lastIndexOf(".gzip"))
+ else R2_name = input_R2
+ R2_ext = R2_name.substring(R2_name.lastIndexOf("."), R2_name.size)
+ R2_name = R2_name.substring(0, R2_name.lastIndexOf(R2_ext))
+ }
}
def script() {
@@ -42,6 +58,12 @@ class Flexiprep(private var globalConfig: Config) extends QScript with BiopetQSc
outputFiles += ("output_R1" -> zcatIfNeeded(input_R1,outputDir))
if (paired) outputFiles += ("output_R2" -> zcatIfNeeded(input_R2,outputDir))
+ addSeqstat(outputFiles("output_R1"), "seqstat_R1")
+ if (paired) addSeqstat(outputFiles("output_R2"), "seqstat_qc_R2")
+
+ addSha1sum(outputFiles("output_R1"), "sha1_R1")
+ if (paired) addSha1sum(outputFiles("output_R2"), "sha1_R2")
+
var results: Map[String,File] = Map()
if (paired) {
results = runTrimClip(outputFiles("output_R1"), outputFiles("output_R2"), outputDir)
@@ -51,36 +73,36 @@ class Flexiprep(private var globalConfig: Config) extends QScript with BiopetQSc
results = runTrimClip(outputFiles("output_R1"), outputDir)
outputFiles += ("output_R1" -> results("output_R1"))
}
- runFinalFastqc()
+ runFinalize(List(outputFiles("output_R1")), List(outputFiles("output_R2")))
}
def runInitialFastqc() {
- var fastqc_R1 = runFastqc(input_R1,outputDir + "/fastqc_R1/")
+ var fastqc_R1 = runFastqc(input_R1,outputDir + "/" + R1_name + ".fastqc/")
outputFiles += ("fastqc_R1" -> fastqc_R1.output)
- outputFiles += ("qualtype_R1" -> getQualtype(fastqc_R1))
- outputFiles += ("contams_R1" -> getContams(fastqc_R1))
+ 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 + "/fastqc_R2/")
+ var fastqc_R2 = runFastqc(input_R2,outputDir + "/" + R2_name + ".fastqc/")
outputFiles += ("fastqc_R2" -> fastqc_R2.output)
- outputFiles += ("qualtype_R2" -> getQualtype(fastqc_R2))
- outputFiles += ("contams_R2" -> getContams(fastqc_R2))
+ outputFiles += ("qualtype_R2" -> getQualtype(fastqc_R2, R2_name))
+ outputFiles += ("contams_R2" -> getContams(fastqc_R2, R2_name))
}
}
- def getQualtype(fastqc:Fastqc): File = {
+ def getQualtype(fastqc:Fastqc, pairname:String): File = {
val fastqcToQualtype = new FastqcToQualtype(config) {
this.fastqc_output = fastqc.output
- this.out = swapExt(outputDir, fastqc.fastqfile, "", ".qualtype.txt")
+ this.out = new File(outputDir + pairname + ".qualtype.txt")
}
add(fastqcToQualtype)
return fastqcToQualtype.out
}
- def getContams(fastqc:Fastqc): File = {
+ def getContams(fastqc:Fastqc, pairname:String): File = {
val fastqcToContams = new FastqcToContams(config) {
this.fastqc_output = fastqc.output
- this.out = swapExt(outputDir, fastqc.fastqfile, "", ".contams.txt")
+ this.out = new File(outputDir + pairname + ".contams.txt")
this.contams_file = fastqc.contaminants
}
add(fastqcToContams)
@@ -92,12 +114,9 @@ class Flexiprep(private var globalConfig: Config) extends QScript with BiopetQSc
}
def runTrimClip(R1_in:File, R2_in:File, outDir:String) : Map[String,File] = {
var results: Map[String,File] = Map()
-
+
var R1: File = new File(R1_in)
var R2: File = new File(R2_in)
- var R1_ext: String = R1.getName().substring(R1.getName().lastIndexOf("."), R1.getName().size)
- var R2_ext: String = ""
- if (paired) R2_ext = R2.getName().substring(R2.getName().lastIndexOf("."), R2.getName().size)
if (!skipClip) { // Adapter clipping
val cutadapt_R1 = new Cutadapt(config) {
@@ -119,9 +138,9 @@ class Flexiprep(private var globalConfig: Config) extends QScript with BiopetQSc
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, ".clip"+R1_ext, ".clipsync"+R1_ext)
- this.output_R2 = swapExt(outDir, R2, ".clip"+R2_ext, ".clipsync"+R2_ext)
- this.output_stats = swapExt(outDir, R1, ".clip"+R1_ext, ".clipsync.stats")
+ 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")
}
add(fastqSync)
R1 = fastqSync.output_R1
@@ -151,11 +170,52 @@ class Flexiprep(private var globalConfig: Config) extends QScript with BiopetQSc
return results
}
- def runFinalFastqc() {
+ def runFinalize(fastq_R1:List[File], fastq_R2:List[File]) {
+ if (fastq_R1.length != fastq_R2.length) throw new IllegalStateException("R1 and R2 file number is not the same")
+ var R1: File = ""
+ var R2: File = ""
+ if (fastq_R1.length == 1) {
+ for (file <- fastq_R1) R1 = file
+ for (file <- fastq_R2) R2 = file
+ } else {
+ throw new IllegalStateException("Not yet inplemented") // For chuncking
+ }
+
+ if (!config.getAsBoolean("skip_native_link", false)) {
+ val lnR1 = new Ln(config) { this.in = R1 }
+ R1 = new File(outputDir + R1_name + ".qc" + R1_ext)
+ lnR1.out = R1
+ add(lnR1)
+ if (paired) {
+ val lnR2 = new Ln(config) { this.in = R2 }
+ R2 = new File(outputDir + R2_name + ".qc" + R2_ext)
+ lnR2.out = R2
+ add(lnR2)
+ }
+ }
+
+ addSeqstat(R1, "seqstat_qc_R1")
+ if (paired) addSeqstat(R2, "seqstat_qc_R2")
+
+ addSha1sum(R1, "sha1_qc_R1")
+ if (paired) addSha1sum(R2, "sha1_qc_R2")
+
if (!skipTrim || !skipClip) {
- outputFiles += ("fastqc_R1_final" -> runFastqc(outputFiles("output_R1"),outputDir + "/fastqc_qc_R1/").output)
- if (paired) outputFiles += ("fastqc_R2_final" -> runFastqc(outputFiles("output_R2"),outputDir + "/fastqc_qc_R2/").output)
+ 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)
+ }
+
+ 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")
}
+ for ((k,v) <- outputFiles) summarize.deps +:= v
+ add(summarize)
}
def runFastqc(fastqfile:File, outDir:String) : Fastqc = {
@@ -183,8 +243,20 @@ class Flexiprep(private var globalConfig: Config) extends QScript with BiopetQSc
} else return file
}
- override def onExecutionDone(jobs: Map[QFunction, JobRunInfo], success: Boolean) {
- logger.info("Flexiprep is done")
+ def addSeqstat(fastq:File, key:String) {
+ val ext = fastq.getName.substring(fastq.getName.lastIndexOf("."))
+ val seqstat = new Seqstat(config) { this.input_fastq = fastq }
+ seqstat.out = swapExt(outputDir, fastq, ext, ".seqstats.json")
+ add(seqstat)
+ outputFiles += (key -> seqstat.out)
+ }
+
+ 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")
+ add(sha1sum)
+ outputFiles += (key -> sha1sum.out)
}
}
--
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