From 29923378a9cc6cb3cf339da7dccd8e8acd87d1a9 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Thu, 15 Oct 2015 13:09:38 +0200
Subject: [PATCH] Fix code warnings
---
.../pipelines/flexiprep/QcCommand.scala | 36 +++++++++----------
1 file changed, 18 insertions(+), 18 deletions(-)
diff --git a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/QcCommand.scala b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/QcCommand.scala
index 253cb60e1..9a82541a4 100644
--- a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/QcCommand.scala
+++ b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/QcCommand.scala
@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep
import java.io.File
import nl.lumc.sasc.biopet.core.summary.{ SummaryQScript, Summarizable }
-import nl.lumc.sasc.biopet.core.{ BiopetFifoPipe, BiopetCommandLineFunction, BiopetPipe }
+import nl.lumc.sasc.biopet.core.{ BiopetFifoPipe, BiopetCommandLineFunction }
import nl.lumc.sasc.biopet.extensions.{ Cat, Gzip, Sickle, Cutadapt }
import nl.lumc.sasc.biopet.extensions.seqtk.SeqtkSeq
import nl.lumc.sasc.biopet.utils.config.Configurable
@@ -73,20 +73,20 @@ class QcCommand(val root: Configurable, val fastqc: Fastqc) extends BiopetComman
case _ => None
}
if (seqtk.Q.isDefined) seqtk.V = true
- seqtk.getVersion
+ addPipeJob(seqtk)
clip = if (!flexiprep.skipClip) {
val foundAdapters = fastqc.foundAdapters.map(_.seq)
if (foundAdapters.nonEmpty) {
- val cutadept = new Cutadapt(root)
- cutadept.fastq_input = seqtk.output
- cutadept.fastq_output = new File(output.getParentFile, input.getName + ".cutadept.fq")
- cutadept.stats_output = new File(flexiprep.outputDir, s"${flexiprep.sampleId.getOrElse("x")}-${flexiprep.libId.getOrElse("x")}.$read.clip.stats")
- if (cutadept.default_clip_mode == "3") cutadept.opt_adapter ++= foundAdapters
- else if (cutadept.default_clip_mode == "5") cutadept.opt_front ++= foundAdapters
- else if (cutadept.default_clip_mode == "both") cutadept.opt_anywhere ++= foundAdapters
- cutadept.getVersion
- Some(cutadept)
+ val cutadapt = new Cutadapt(root)
+ cutadapt.fastq_input = seqtk.output
+ cutadapt.fastq_output = new File(output.getParentFile, input.getName + ".cutadapt.fq")
+ cutadapt.stats_output = new File(flexiprep.outputDir, s"${flexiprep.sampleId.getOrElse("x")}-${flexiprep.libId.getOrElse("x")}.$read.clip.stats")
+ if (cutadapt.default_clip_mode == "3") cutadapt.opt_adapter ++= foundAdapters
+ else if (cutadapt.default_clip_mode == "5") cutadapt.opt_front ++= foundAdapters
+ else if (cutadapt.default_clip_mode == "both") cutadapt.opt_anywhere ++= foundAdapters
+ addPipeJob(cutadapt)
+ Some(cutadapt)
} else None
} else None
@@ -94,17 +94,17 @@ class QcCommand(val root: Configurable, val fastqc: Fastqc) extends BiopetComman
val sickle = new Sickle(root)
sickle.output_stats = new File(flexiprep.outputDir, s"${flexiprep.sampleId.getOrElse("x")}-${flexiprep.libId.getOrElse("x")}.$read.trim.stats")
sickle.input_R1 = clip match {
- case Some(clip) => clip.fastq_output
+ case Some(c) => c.fastq_output
case _ => seqtk.output
}
sickle.output_R1 = new File(output.getParentFile, input.getName + ".sickle.fq")
- sickle.getVersion
+ addPipeJob(sickle)
Some(sickle)
} else None
val outputFile = (clip, trim) match {
- case (_, Some(trim)) => trim.output_R1
- case (Some(clip), _) => clip.fastq_output
+ case (_, Some(t)) => t.output_R1
+ case (Some(c), _) => c.fastq_output
case _ => seqtk.output
}
@@ -134,9 +134,9 @@ class QcCommand(val root: Configurable, val fastqc: Fastqc) extends BiopetComman
def cmdLine = {
val cmd = (clip, trim) match {
- case (Some(clip), Some(trim)) => new BiopetFifoPipe(root, seqtk :: clip :: trim :: outputCommand :: Nil)
- case (Some(clip), _) => new BiopetFifoPipe(root, seqtk :: clip :: outputCommand :: Nil)
- case (_, Some(trim)) => new BiopetFifoPipe(root, seqtk :: trim :: outputCommand :: Nil)
+ case (Some(c), Some(t)) => new BiopetFifoPipe(root, seqtk :: c :: t :: outputCommand :: Nil)
+ case (Some(c), _) => new BiopetFifoPipe(root, seqtk :: c :: outputCommand :: Nil)
+ case (_, Some(t)) => new BiopetFifoPipe(root, seqtk :: t :: outputCommand :: Nil)
case _ => new BiopetFifoPipe(root, seqtk :: outputCommand :: Nil)
}
--
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