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biopet.biopet
Commits
097f37b0
Commit
097f37b0
authored
Feb 16, 2016
by
Peter van 't Hof
Browse files
Added check abort step in pipeline
parent
7c863726
Changes
4
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public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/ValidateFastq.scala
View file @
097f37b0
...
...
@@ -17,9 +17,9 @@ package nl.lumc.sasc.biopet.extensions.tools
import
java.io.File
import
nl.lumc.sasc.biopet.core.
{
Reference
,
ToolCommandFunction
}
import
nl.lumc.sasc.biopet.core.
{
Reference
,
ToolCommandFunction
}
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
class
ValidateFastq
(
val
root
:
Configurable
)
extends
ToolCommandFunction
{
def
toolObject
=
nl
.
lumc
.
sasc
.
biopet
.
tools
.
ValidateFastq
...
...
public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/ValidateFastq.scala
View file @
097f37b0
...
...
@@ -96,10 +96,10 @@ object ValidateFastq extends ToolCommand {
private
var
maxQual
:
Option
[
Char
]
=
None
/**
*
* @param record
* @throws IllegalStateException
*/
*
* @param record
* @throws IllegalStateException
*/
private
[
tools
]
def
checkQualEncoding
(
record
:
FastqRecord
)
:
Unit
=
{
val
min
=
record
.
getBaseQualityString
.
min
val
max
=
record
.
getBaseQualityString
.
max
...
...
@@ -114,10 +114,10 @@ object ValidateFastq extends ToolCommand {
}
/**
*
* @return
* @throws IllegalStateException
*/
*
* @return
* @throws IllegalStateException
*/
private
[
tools
]
def
getPossibleEncodings
:
List
[
String
]
=
{
val
buffer
:
ListBuffer
[
String
]
=
ListBuffer
()
(
minQual
,
maxQual
)
match
{
...
...
public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/CheckValidateFastq.scala
0 → 100644
View file @
097f37b0
/**
* 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.pipelines.flexiprep
import
java.io.File
import
nl.lumc.sasc.biopet.core.summary.WriteSummary
import
org.broadinstitute.gatk.queue.function.InProcessFunction
import
org.broadinstitute.gatk.utils.commandline.
{
Argument
,
Input
}
import
scala.io.Source
/**
* This class checks md5sums and give an exit code 1 when md5sum is not the same
*
* Created by pjvanthof on 16/08/15.
*/
class
CheckValidateFastq
extends
InProcessFunction
{
@Input
(
required
=
true
)
var
inputLogFile
:
File
=
_
/** Exits whenever the input md5sum is not the same as the output md5sum */
def
run
:
Unit
=
{
val
reader
=
Source
.
fromFile
(
inputLogFile
)
reader
.
getLines
().
foreach
{
line
=>
if
(
line
.
startsWith
(
"ERROR"
))
{
logger
.
error
(
"Corrupt fastq file found, aborting pipeline"
)
// 130 Simulates a ctr-C
Runtime
.
getRuntime
.
halt
(
130
)
}
}
reader
.
close
()
}
}
\ No newline at end of file
public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
View file @
097f37b0
...
...
@@ -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.
{
ValidateFastq
,
SeqStat
,
FastqSync
}
import
nl.lumc.sasc.biopet.extensions.tools.
{
ValidateFastq
,
SeqStat
,
FastqSync
}
import
org.broadinstitute.gatk.queue.QScript
...
...
@@ -120,6 +120,11 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
validateFastq
.
jobOutputFile
=
new
File
(
outputDir
,
".validate_fastq.log.out"
)
add
(
validateFastq
)
val
checkValidateFastq
=
new
CheckValidateFastq
checkValidateFastq
.
inputLogFile
=
validateFastq
.
jobOutputFile
checkValidateFastq
.
jobOutputFile
=
new
File
(
outputDir
,
".check.validate_fastq.log.out"
)
add
(
checkValidateFastq
)
if
(
paired
)
{
fastqc_R2
=
Fastqc
(
this
,
input_R2
.
get
,
new
File
(
outputDir
,
R2_name
+
".fastqc/"
))
add
(
fastqc_R2
)
...
...
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