From cde8f1a6c35911120d75e8e3b3f4badb1c4c9562 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Mon, 28 Jul 2014 14:31:28 +0200
Subject: [PATCH] Fix on fastqc jobs
---
.../nl/lumc/sasc/biopet/function/fastq/Fastqc.scala | 2 +-
.../sasc/biopet/pipelines/flexiprep/Flexiprep.scala | 13 ++++++++++---
2 files changed, 11 insertions(+), 4 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 cc48a1682..ca30614d1 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.jobOutputFile = new File(outDir + "/" + filename + "_fastqc.zip")
+ fastqcCommand.output = 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 ecc911a77..f2fc812ee 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
@@ -82,12 +82,14 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
if (paired) addSha1sum(outputFiles("fastq_input_R2"), "sha1_R2")
var fastqc_R1 = Fastqc(this, input_R1, outputDir + "/" + R1_name + ".fastqc/")
+ add(fastqc_R1)
outputFiles += ("fastqc_R1" -> fastqc_R1.output)
outputFiles += ("qualtype_R1" -> getQualtype(fastqc_R1, R1_name))
outputFiles += ("contams_R1" -> getContams(fastqc_R1, R1_name))
if (paired) {
var fastqc_R2 = Fastqc(this, input_R2, outputDir + "/" + R2_name + ".fastqc/")
+ add(fastqc_R2)
outputFiles += ("fastqc_R2" -> fastqc_R2.output)
outputFiles += ("qualtype_R2" -> getQualtype(fastqc_R2, R2_name))
outputFiles += ("contams_R2" -> getContams(fastqc_R2, R2_name))
@@ -232,9 +234,14 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
addSha1sum(R1, "sha1_qc_R1")
if (paired) addSha1sum(R2, "sha1_qc_R2")
-
- 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)
+ 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)
+ }
}
if (!skipSummary) {
--
GitLab