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biopet.biopet
Commits
7c863726
Commit
7c863726
authored
Feb 16, 2016
by
Peter van 't Hof
Browse files
Adding ValidateFastq to flexiprep
parent
46599c3f
Changes
2
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public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/ValidateFastq.scala
0 → 100644
View file @
7c863726
/**
* Biopet is built on top of GATK Queue for building bioinformatic
* pipelines. It is mainly intended to support LUMC SHARK cluster which is running
* SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
* should also be able to execute Biopet tools and pipelines.
*
* Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
*
* Contact us at: sasc@lumc.nl
*
* A dual licensing mode is applied. The source code within this project that are
* not part of GATK Queue is freely available for non-commercial use under an AGPL
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
package
nl.lumc.sasc.biopet.extensions.tools
import
java.io.File
import
nl.lumc.sasc.biopet.core.
{
Reference
,
ToolCommandFunction
}
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
class
ValidateFastq
(
val
root
:
Configurable
)
extends
ToolCommandFunction
{
def
toolObject
=
nl
.
lumc
.
sasc
.
biopet
.
tools
.
ValidateFastq
@Input
(
doc
=
"Input R1 fastq file"
,
required
=
true
)
var
r1Fastq
:
File
=
_
@Input
(
doc
=
"Input R1 fastq file"
,
required
=
false
)
var
r2Fastq
:
Option
[
File
]
=
None
override
def
cmdLine
=
super
.
cmdLine
+
required
(
"-i"
,
r1Fastq
)
+
optional
(
"-j"
,
r2Fastq
)
}
public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
View file @
7c863726
...
...
@@ -20,7 +20,7 @@ import nl.lumc.sasc.biopet.core.{ BiopetFifoPipe, PipelineCommand, SampleLibrary
import
nl.lumc.sasc.biopet.extensions.
{
Zcat
,
Gzip
}
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
nl.lumc.sasc.biopet.utils.IoUtils._
import
nl.lumc.sasc.biopet.extensions.tools.
{
SeqStat
,
FastqSync
}
import
nl.lumc.sasc.biopet.extensions.tools.
{
ValidateFastq
,
SeqStat
,
FastqSync
}
import
org.broadinstitute.gatk.queue.QScript
...
...
@@ -114,6 +114,12 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
addSummarizable
(
fastqc_R1
,
"fastqc_R1"
)
outputFiles
+=
(
"fastqc_R1"
->
fastqc_R1
.
output
)
val
validateFastq
=
new
ValidateFastq
(
this
)
validateFastq
.
r1Fastq
=
input_R1
validateFastq
.
r2Fastq
=
input_R2
validateFastq
.
jobOutputFile
=
new
File
(
outputDir
,
".validate_fastq.log.out"
)
add
(
validateFastq
)
if
(
paired
)
{
fastqc_R2
=
Fastqc
(
this
,
input_R2
.
get
,
new
File
(
outputDir
,
R2_name
+
".fastqc/"
))
add
(
fastqc_R2
)
...
...
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