From 7c1fa2552ee44eba4ee76717583a216234613a67 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Mon, 4 Aug 2014 12:02:53 +0200
Subject: [PATCH] Use of new constructors
---
.../pipelines/flexiprep/Flexiprep.scala | 69 +++++++------------
1 file changed, 25 insertions(+), 44 deletions(-)
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 031eab734..5075f3d24 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
@@ -3,9 +3,9 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep
import org.broadinstitute.gatk.queue.QScript
import org.broadinstitute.gatk.utils.commandline.{ Input, Argument }
-import nl.lumc.sasc.biopet.core.{BiopetQScript, PipelineCommand}
+import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
import nl.lumc.sasc.biopet.core.config.Configurable
-import nl.lumc.sasc.biopet.extensions.{Cat, Ln, Pbzip2, Sha1sum, Zcat}
+import nl.lumc.sasc.biopet.extensions.{ Cat, Ln, Pbzip2, Sha1sum, Zcat }
import nl.lumc.sasc.biopet.pipelines.flexiprep.scripts._
class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
@@ -141,7 +141,8 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
var R1: File = new File(R1_in)
var R2: File = new File(R2_in)
-
+ var deps: List[File] = if (paired) List(R1, R2) else List(R1)
+
val seqstat_R1 = Seqstat(this, R1, fastqc_R1, outDir)
add(seqstat_R1)
summary.addSeqstat(seqstat_R1, R2 = false, after = false, chunk)
@@ -154,63 +155,50 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
if (!skipClip) { // Adapter clipping
- val cutadapt_R1 = new Cutadapt(this)
-
+ val cutadapt_R1 = Cutadapt(this, R1, swapExt(outDir, R1, R1_ext, ".clip" + R1_ext))
if (!skipTrim || paired) cutadapt_R1.isIntermediate = true
- cutadapt_R1.fastq_input = R1
- cutadapt_R1.fastq_output = swapExt(outDir, R1, R1_ext, ".clip" + R1_ext)
- cutadapt_R1.stats_output = swapExt(outDir, R1, R1_ext, ".clip.stats")
- outputFiles += ("cutadapt_R1_stats" -> cutadapt_R1.stats_output)
-
if (outputFiles.contains("contams_R1")) cutadapt_R1.contams_file = outputFiles("contams_R1")
-
add(cutadapt_R1)
summary.addCutadapt(cutadapt_R1, R2 = false, chunk)
R1 = cutadapt_R1.fastq_output
+ deps ::= R1
+ outputFiles += ("cutadapt_R1_stats" -> cutadapt_R1.stats_output)
if (paired) {
- val cutadapt_R2 = new Cutadapt(this)
+ val cutadapt_R2 = Cutadapt(this, R2, swapExt(outDir, R2, R2_ext, ".clip" + R2_ext))
if (!skipTrim || paired) cutadapt_R2.isIntermediate = true
- cutadapt_R2.fastq_input = R2
- cutadapt_R2.fastq_output = swapExt(outDir, R2, R2_ext, ".clip" + R2_ext)
- cutadapt_R2.stats_output = swapExt(outDir, R2, R2_ext, ".clip.stats")
outputFiles += ("cutadapt_R2_stats" -> cutadapt_R2.stats_output)
if (outputFiles.contains("contams_R2")) cutadapt_R2.contams_file = outputFiles("contams_R2")
add(cutadapt_R2)
summary.addCutadapt(cutadapt_R2, R2 = true, chunk)
R2 = cutadapt_R2.fastq_output
- val fastqSync = new FastqSync(this)
+ deps ::= R2
+
+ val fastqSync = FastqSync(this, cutadapt_R1.fastq_input, cutadapt_R1.fastq_output, cutadapt_R2.fastq_output,
+ swapExt(outDir, R1, R1_ext, ".sync" + R1_ext), swapExt(outDir, R2, R2_ext, ".sync" + R2_ext), swapExt(outDir, R1, R1_ext, ".sync.stats"))
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
- 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")
+ fastqSync.deps :::= deps
add(fastqSync)
summary.addFastqcSync(fastqSync, chunk)
outputFiles += ("syncStats" -> fastqSync.output_stats)
R1 = fastqSync.output_R1
R2 = fastqSync.output_R2
+ deps :::= R1 :: R2 :: Nil
}
}
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)
- if (!skipClip) sickle.deps :+= R2_in
}
sickle.output_stats = swapExt(outDir, R1, R1_ext, ".trim.stats")
+ sickle.deps = deps
add(sickle)
summary.addSickle(sickle, chunk)
R1 = sickle.output_R1
@@ -218,11 +206,13 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
}
val seqstat_R1_after = Seqstat(this, R1, fastqc_R1, outDir)
+ seqstat_R1_after.deps = deps
add(seqstat_R1_after)
summary.addSeqstat(seqstat_R1_after, R2 = false, after = true, chunk)
if (paired) {
val seqstat_R2_after = Seqstat(this, R2, fastqc_R2, outDir)
+ seqstat_R2_after.deps = deps
add(seqstat_R2_after)
summary.addSeqstat(seqstat_R2_after, R2 = true, after = true, chunk)
}
@@ -237,33 +227,25 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
var R1: File = ""
var R2: File = ""
if (fastq_R1.length == 1) {
- for (file <- fastq_R1) R1 = file
- for (file <- fastq_R2) R2 = file
+ R1 = fastq_R1.head
+ R2 = fastq_R2.head
} else {
R1 = new File(outputDir + R1_name + ".qc" + R1_ext)
- logger.debug(fastq_R1)
add(Cat(this, fastq_R1, R1), true)
if (paired) {
- logger.debug(fastq_R2)
R2 = new File(outputDir + R2_name + ".qc" + R2_ext)
add(Cat(this, fastq_R2, R2), true)
}
}
if (fastq_R1.length == 1 && !config("skip_native_link", default = false)) {
- val lnR1 = new Ln(this)
- lnR1.in = R1
- R1 = new File(outputDir + R1_name + ".qc" + R1_ext)
- lnR1.out = R1
- lnR1.relative = true
- add(lnR1)
+ val newFile = new File(outputDir + R1_name + ".qc" + R1_ext)
+ add(Ln(this, R1, newFile))
+ R1 = newFile
if (paired) {
- val lnR2 = new Ln(this)
- lnR2.in = R2
- lnR2.relative = true
- R2 = new File(outputDir + R2_name + ".qc" + R2_ext)
- lnR2.out = R2
- add(lnR2)
+ val newFile = new File(outputDir + R2_name + ".qc" + R2_ext)
+ add(Ln(this, R2, newFile))
+ R2 = newFile
}
}
@@ -271,7 +253,6 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
if (paired) outputFiles += ("output_R2" -> R2)
if (!skipTrim || !skipClip) {
-
val sha1sum_R1 = Sha1sum(this, R1, outputDir)
add(sha1sum_R1)
summary.addSha1sum(sha1sum_R1, R2 = false, after = true)
--
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