From e2a873b6046babb67fdde267c7d787e099b89e4a Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Thu, 15 Oct 2015 11:15:34 +0200
Subject: [PATCH] Fixed version to single end executables
---
.../nl/lumc/sasc/biopet/pipelines/flexiprep/QcCommand.scala | 3 +++
1 file changed, 3 insertions(+)
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 3e516b638..253cb60e1 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
@@ -73,6 +73,7 @@ class QcCommand(val root: Configurable, val fastqc: Fastqc) extends BiopetComman
case _ => None
}
if (seqtk.Q.isDefined) seqtk.V = true
+ seqtk.getVersion
clip = if (!flexiprep.skipClip) {
val foundAdapters = fastqc.foundAdapters.map(_.seq)
@@ -84,6 +85,7 @@ class QcCommand(val root: Configurable, val fastqc: Fastqc) extends BiopetComman
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)
} else None
} else None
@@ -96,6 +98,7 @@ class QcCommand(val root: Configurable, val fastqc: Fastqc) extends BiopetComman
case _ => seqtk.output
}
sickle.output_R1 = new File(output.getParentFile, input.getName + ".sickle.fq")
+ sickle.getVersion
Some(sickle)
} else None
--
GitLab