From 373dbb5c08832e573708aabf86b080826352dd20 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Mon, 28 Jul 2014 14:22:48 +0200
Subject: [PATCH] Revert "Fix on fastqc jobs"
This reverts commit 5945ab1746a433f4c9c2100176934d7ee86c38a2.
---
.../sasc/biopet/function/fastq/Fastqc.scala | 2 +-
.../biopet/pipelines/flexiprep/Flexiprep.scala | 18 +++++-------------
2 files changed, 6 insertions(+), 14 deletions(-)
diff --git a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Fastqc.scala b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Fastqc.scala
index ca30614d1..cc48a1682 100644
--- a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Fastqc.scala
+++ b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Fastqc.scala
@@ -62,7 +62,7 @@ object Fastqc {
if (filename.endsWith(".gzip")) filename = filename.substring(0, filename.size - 5)
if (filename.endsWith(".fastq")) filename = filename.substring(0, filename.size - 6)
//if (filename.endsWith(".fq")) filename = filename.substring(0,filename.size - 3)
- fastqcCommand.output = new File(outDir + "/" + filename + "_fastqc.zip")
+ fastqcCommand.jobOutputFile = new File(outDir + "/" + filename + "_fastqc.zip")
fastqcCommand.afterGraph
return fastqcCommand
}
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 3e0aeac23..ecc911a77 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
@@ -81,18 +81,16 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
addSha1sum(outputFiles("fastq_input_R1"), "sha1_R1")
if (paired) addSha1sum(outputFiles("fastq_input_R2"), "sha1_R2")
- val fastqc_R1 = Fastqc(this, input_R1, outputDir + "/" + R1_name + ".fastqc/")
+ var fastqc_R1 = Fastqc(this, input_R1, outputDir + "/" + R1_name + ".fastqc/")
outputFiles += ("fastqc_R1" -> fastqc_R1.output)
outputFiles += ("qualtype_R1" -> getQualtype(fastqc_R1, R1_name))
outputFiles += ("contams_R1" -> getContams(fastqc_R1, R1_name))
- add(fastqc_R1)
-
+
if (paired) {
- val fastqc_R2 = Fastqc(this, input_R2, outputDir + "/" + R2_name + ".fastqc/")
+ var fastqc_R2 = Fastqc(this, input_R2, outputDir + "/" + R2_name + ".fastqc/")
outputFiles += ("fastqc_R2" -> fastqc_R2.output)
outputFiles += ("qualtype_R2" -> getQualtype(fastqc_R2, R2_name))
outputFiles += ("contams_R2" -> getContams(fastqc_R2, R2_name))
- add(fastqc_R2)
}
}
@@ -235,14 +233,8 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
addSha1sum(R1, "sha1_qc_R1")
if (paired) addSha1sum(R2, "sha1_qc_R2")
- val fastqc_R1 = Fastqc(this, outputFiles("output_R1"), outputDir + "/" + R1_name + ".qc.fastqc/")
- add(fastqc_R1)
- outputFiles += ("fastqc_R1_final" -> fastqc_R1.output)
- if (paired) {
- val fastqc_R2 = Fastqc(this, outputFiles("output_R2"), outputDir + "/" + R2_name + ".qc.fastqc/")
- add(fastqc_R2)
- outputFiles += ("fastqc_R2_final" -> fastqc_R2.output)
- }
+ outputFiles += ("fastqc_R1_final" -> Fastqc(this, outputFiles("output_R1"), outputDir + "/" + R1_name + ".qc.fastqc/").output)
+ if (paired) outputFiles += ("fastqc_R2_final" -> Fastqc(this, outputFiles("output_R2"), outputDir + "/" + R2_name + ".qc.fastqc/").output)
}
if (!skipSummary) {
--
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