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Mirrors
biopet.biopet
Commits
95ba716f
Commit
95ba716f
authored
Jul 21, 2014
by
Peter van 't Hof
Browse files
Spelling error
parent
2f47af7e
Changes
19
Hide whitespace changes
Inline
Side-by-side
bam-metrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
View file @
95ba716f
...
...
@@ -7,7 +7,7 @@ import java.io.File
import
nl.lumc.sasc.biopet.core.apps.
{
BedToInterval
,
BiopetFlagstat
}
import
nl.lumc.sasc.biopet.core.config.Configurable
import
nl.lumc.sasc.biopet.function.bedtools.
{
BedtoolsCoverage
,
BedtoolsIntersect
}
import
nl.lumc.sasc.biopet.function.picard.
{
CollectInsertSizeMetrics
,
CollectGcBiasMetrics
,
CalculateHsMetrics
}
import
nl.lumc.sasc.biopet.function.picard.
{
CollectInsertSizeMetrics
,
CollectGcBiasMetrics
,
CalculateHsMetrics
,
CollectAlignmentSummaryMetrics
}
import
nl.lumc.sasc.biopet.function.samtools.SamtoolsFlagstat
class
BamMetrics
(
val
root
:
Configurable
)
extends
QScript
with
BiopetQScript
{
...
...
@@ -36,6 +36,7 @@ class BamMetrics(val root:Configurable) extends QScript with BiopetQScript {
add
(
BiopetFlagstat
(
this
,
inputBam
,
outputDir
))
add
(
CollectGcBiasMetrics
(
this
,
inputBam
,
outputDir
))
add
(
CollectInsertSizeMetrics
(
this
,
inputBam
,
outputDir
))
add
(
CollectAlignmentSummaryMetrics
(
this
,
inputBam
,
outputDir
))
val
baitIntervalFile
=
if
(
baitBedFile
!=
null
)
new
File
(
outputDir
,
baitBedFile
.
getName
.
stripSuffix
(
".bed"
)
+
".interval"
)
else
null
if
(
baitIntervalFile
!=
null
)
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
View file @
95ba716f
...
...
@@ -22,8 +22,8 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
var
vmem
:
String
=
_
val
defaultVmem
:
String
=
""
@Argument
(
doc
=
"Execut
e
ble"
)
var
execut
e
ble
:
String
=
_
@Argument
(
doc
=
"Execut
a
ble"
)
var
execut
a
ble
:
String
=
_
protected
def
beforeCmd
{
}
...
...
@@ -32,7 +32,7 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
}
override
def
freezeFieldValues
()
{
checkExecut
e
ble
checkExecut
a
ble
afterGraph
jobOutputFile
=
new
File
(
firstOutput
.
getParent
+
"/."
+
firstOutput
.
getName
+
"."
+
analysisName
+
".out"
)
...
...
@@ -49,26 +49,26 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
super
.
freezeFieldValues
()
}
protected
def
checkExecut
e
ble
{
try
if
(
execut
e
ble
!=
null
)
{
protected
def
checkExecut
a
ble
{
try
if
(
execut
a
ble
!=
null
)
{
val
buffer
=
new
StringBuffer
()
val
cmd
=
Seq
(
"which"
,
execut
e
ble
)
val
cmd
=
Seq
(
"which"
,
execut
a
ble
)
val
process
=
Process
(
cmd
).
run
(
ProcessLogger
(
buffer
.
append
(
_
)))
if
(
process
.
exitValue
==
0
)
{
execut
e
ble
=
buffer
.
toString
val
file
=
new
File
(
execut
e
ble
)
execut
e
ble
=
file
.
getCanonicalPath
execut
a
ble
=
buffer
.
toString
val
file
=
new
File
(
execut
a
ble
)
execut
a
ble
=
file
.
getCanonicalPath
}
else
{
logger
.
error
(
"execut
e
ble: '"
+
execut
e
ble
+
"' not found, please check config"
)
throw
new
QException
(
"execut
e
ble: '"
+
execut
e
ble
+
"' not found, please check config"
)
logger
.
error
(
"execut
a
ble: '"
+
execut
a
ble
+
"' not found, please check config"
)
throw
new
QException
(
"execut
a
ble: '"
+
execut
a
ble
+
"' not found, please check config"
)
}
}
catch
{
case
ioe
:
java.io.IOException
=>
logger
.
warn
(
"Could not use 'which', check on execut
e
ble skipped: "
+
ioe
)
case
ioe
:
java.io.IOException
=>
logger
.
warn
(
"Could not use 'which', check on execut
a
ble skipped: "
+
ioe
)
}
}
final
protected
def
preCmdInternal
{
checkExecut
e
ble
checkExecut
a
ble
//for (input <- this.inputs) if (!input.exists) throw new IllegalStateException("Input: " + input + " for " + analysisName + " is missing")
//logger.debug("Config for " + analysisName + ": " + localConfig)
...
...
@@ -96,7 +96,7 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
case
_
=>
}
}
logger
.
warn
(
"Version command: '"
+
versionCommand
+
"' give a exit code "
+
process
.
exitValue
+
" but no version was found, execut
e
ble oke?"
)
logger
.
warn
(
"Version command: '"
+
versionCommand
+
"' give a exit code "
+
process
.
exitValue
+
" but no version was found, execut
a
ble oke?"
)
return
"N/A"
}
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala
View file @
95ba716f
...
...
@@ -3,12 +3,12 @@ package nl.lumc.sasc.biopet.core
import
org.broadinstitute.gatk.queue.function.JavaCommandLineFunction
abstract
class
BiopetJavaCommandLineFunction
extends
JavaCommandLineFunction
with
BiopetCommandLineFunctionTrait
{
execut
e
ble
=
"java"
execut
a
ble
=
"java"
override
def
commandLine
:
String
=
{
preCmdInternal
val
cmd
=
super
.
commandLine
val
finalCmd
=
execut
e
ble
+
cmd
.
substring
(
cmd
.
indexOf
(
" "
))
val
finalCmd
=
execut
a
ble
+
cmd
.
substring
(
cmd
.
indexOf
(
" "
))
// addJobReportBinding("command", cmd)
return
cmd
}
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Cat.scala
View file @
95ba716f
...
...
@@ -12,9 +12,9 @@ class Cat(val root:Configurable) extends BiopetCommandLineFunction {
@Output
(
doc
=
"Unzipped file"
,
required
=
true
)
var
output
:
File
=
_
execut
e
ble
=
config
(
"exe"
,
"cat"
)
execut
a
ble
=
config
(
"exe"
,
"cat"
)
def
cmdLine
=
required
(
execut
e
ble
)
+
repeat
(
input
)
+
" > "
+
required
(
output
)
def
cmdLine
=
required
(
execut
a
ble
)
+
repeat
(
input
)
+
" > "
+
required
(
output
)
}
object
Cat
{
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Pbzip2.scala
View file @
95ba716f
...
...
@@ -13,7 +13,7 @@ class Pbzip2(val root:Configurable) extends BiopetCommandLineFunction {
@Output
(
doc
=
"Unzipped file"
)
var
output
:
File
=
_
execut
e
ble
=
config
(
"exe"
,
"pbzip2"
)
execut
a
ble
=
config
(
"exe"
,
"pbzip2"
)
var
decomrpess
=
true
var
memory
:
Int
=
config
(
"memory"
,
1000
)
...
...
@@ -25,7 +25,7 @@ class Pbzip2(val root:Configurable) extends BiopetCommandLineFunction {
memory
=
memory
*
threads
}
def
cmdLine
=
required
(
execut
e
ble
)
+
def
cmdLine
=
required
(
execut
a
ble
)
+
conditional
(
decomrpess
,
"-d"
)
+
conditional
(!
decomrpess
,
"-z"
)
+
optional
(
"-p"
,
threads
,
spaceSeparated
=
false
)
+
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/PythonCommandLineFunction.scala
View file @
95ba716f
...
...
@@ -10,7 +10,7 @@ trait PythonCommandLineFunction extends BiopetCommandLineFunction {
@Input
(
doc
=
"Python script"
,
required
=
false
)
var
python_script
:
File
=
_
execut
e
ble
=
config
(
"python_exe"
,
"python"
)
execut
a
ble
=
config
(
"python_exe"
,
"python"
)
protected
var
python_script_name
:
String
=
_
def
setPythonScript
(
script
:
String
)
{
setPythonScript
(
script
,
""
)
}
...
...
@@ -25,6 +25,6 @@ trait PythonCommandLineFunction extends BiopetCommandLineFunction {
}
def
getPythonCommand
()
:
String
=
{
required
(
execut
e
ble
)
+
required
(
python_script
)
required
(
execut
a
ble
)
+
required
(
python_script
)
}
}
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Sha1sum.scala
View file @
95ba716f
...
...
@@ -12,7 +12,7 @@ class Sha1sum(val root:Configurable) extends BiopetCommandLineFunction {
@Output
(
doc
=
"Unzipped file"
)
var
output
:
File
=
_
execut
e
ble
=
config
(
"exe"
,
"sha1sum"
)
execut
a
ble
=
config
(
"exe"
,
"sha1sum"
)
def
cmdLine
=
required
(
execut
e
ble
)
+
required
(
input
)
+
" > "
+
required
(
output
)
def
cmdLine
=
required
(
execut
a
ble
)
+
required
(
input
)
+
" > "
+
required
(
output
)
}
\ No newline at end of file
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Zcat.scala
View file @
95ba716f
...
...
@@ -12,9 +12,9 @@ class Zcat(val root:Configurable) extends BiopetCommandLineFunction {
@Output
(
doc
=
"Unzipped file"
)
var
output
:
File
=
_
execut
e
ble
=
config
(
"exe"
,
"zcat"
)
execut
a
ble
=
config
(
"exe"
,
"zcat"
)
def
cmdLine
=
required
(
execut
e
ble
)
+
required
(
input
)
+
" > "
+
required
(
output
)
def
cmdLine
=
required
(
execut
a
ble
)
+
required
(
input
)
+
" > "
+
required
(
output
)
}
object
Zcat
{
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/bedtools/Bedtools.scala
View file @
95ba716f
...
...
@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.function.bedtools
import
nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
abstract
class
Bedtools
extends
BiopetCommandLineFunction
{
execut
e
ble
=
config
(
"exe"
,
"bedtools"
,
"bedtools"
)
override
def
versionCommand
=
execut
e
ble
+
" --version"
execut
a
ble
=
config
(
"exe"
,
"bedtools"
,
"bedtools"
)
override
def
versionCommand
=
execut
a
ble
+
" --version"
override
val
versionRegex
=
"""bedtools (.*)"""
.
r
}
\ No newline at end of file
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/bedtools/BedtoolsCoverage.scala
View file @
95ba716f
...
...
@@ -23,7 +23,7 @@ class BedtoolsCoverage(val root:Configurable) extends Bedtools {
if
(
input
.
getName
.
endsWith
(
".bam"
))
inputTag
=
"-abam"
}
def
cmdLine
=
required
(
execut
e
ble
)
+
required
(
"coverage"
)
+
def
cmdLine
=
required
(
execut
a
ble
)
+
required
(
"coverage"
)
+
required
(
inputTag
,
input
)
+
required
(
"-b"
,
intersectFile
)
+
conditional
(
depth
,
"-d"
)
+
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/bedtools/BedtoolsIntersect.scala
View file @
95ba716f
...
...
@@ -26,7 +26,7 @@ class BedtoolsIntersect(val root:Configurable) extends Bedtools {
if
(
input
.
getName
.
endsWith
(
".bam"
))
inputTag
=
"-abam"
}
def
cmdLine
=
required
(
execut
e
ble
)
+
required
(
"intersect"
)
+
def
cmdLine
=
required
(
execut
a
ble
)
+
required
(
"intersect"
)
+
required
(
inputTag
,
input
)
+
required
(
"-b"
,
intersectFile
)
+
required
(
"-f"
,
minOverlap
)
+
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/picard/Picard.scala
View file @
95ba716f
...
...
@@ -25,7 +25,7 @@ trait Picard extends BiopetJavaCommandLineFunction {
@Argument
(
doc
=
"CREATE_MD5_FILE"
,
required
=
false
)
var
createMd5
:
Boolean
=
config
(
"createmd5"
,
false
,
"picard"
)
override
def
versionCommand
=
execut
e
ble
+
" "
+
javaOpts
+
" "
+
javaExecutable
+
" -h"
override
def
versionCommand
=
execut
a
ble
+
" "
+
javaOpts
+
" "
+
javaExecutable
+
" -h"
override
val
versionRegex
=
"""Version: (.*)"""
.
r
override
val
versionExitcode
=
List
(
0
,
1
)
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/samtools/Samtools.scala
View file @
95ba716f
...
...
@@ -3,8 +3,8 @@ package nl.lumc.sasc.biopet.function.samtools
import
nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
abstract
class
Samtools
extends
BiopetCommandLineFunction
{
execut
e
ble
=
config
(
"exe"
,
"samtools"
,
"samtools"
)
override
def
versionCommand
=
execut
e
ble
execut
a
ble
=
config
(
"exe"
,
"samtools"
,
"samtools"
)
override
def
versionCommand
=
execut
a
ble
override
val
versionRegex
=
"""Version: (.*)"""
.
r
override
val
versionExitcode
=
List
(
0
,
1
)
}
\ No newline at end of file
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/samtools/SamtoolsFlagstat.scala
View file @
95ba716f
...
...
@@ -11,7 +11,7 @@ class SamtoolsFlagstat(val root:Configurable) extends Samtools {
@Output
(
doc
=
"output File"
)
var
output
:
File
=
_
def
cmdLine
=
required
(
execut
e
ble
)
+
required
(
"flagstat"
)
+
required
(
input
)
+
" > "
+
required
(
output
)
def
cmdLine
=
required
(
execut
a
ble
)
+
required
(
"flagstat"
)
+
required
(
input
)
+
" > "
+
required
(
output
)
}
object
SamtoolsFlagstat
{
...
...
flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Cutadapt.scala
View file @
95ba716f
...
...
@@ -17,8 +17,8 @@ class Cutadapt(val root:Configurable) extends BiopetCommandLineFunction {
@Output
(
doc
=
"Output fastq file"
)
var
fastq_output
:
File
=
_
execut
e
ble
=
config
(
"exe"
,
"cutadapt"
)
override
def
versionCommand
=
execut
e
ble
+
" --version"
execut
a
ble
=
config
(
"exe"
,
"cutadapt"
)
override
def
versionCommand
=
execut
a
ble
+
" --version"
override
val
versionRegex
=
"""(.*)"""
.
r
var
default_clip_mode
:
String
=
config
(
"default_clip_mode"
,
"3"
)
...
...
@@ -37,7 +37,7 @@ class Cutadapt(val root:Configurable) extends BiopetCommandLineFunction {
def
cmdLine
=
{
if
(!
opt_adapter
.
isEmpty
||
!
opt_anywhere
.
isEmpty
||
!
opt_front
.
isEmpty
)
{
analysisName
=
getClass
.
getName
required
(
execut
e
ble
)
+
required
(
execut
a
ble
)
+
// options
repeat
(
"-a"
,
opt_adapter
)
+
repeat
(
"-b"
,
opt_anywhere
)
+
...
...
flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Fastqc.scala
View file @
95ba716f
...
...
@@ -17,7 +17,7 @@ class Fastqc(val root:Configurable) extends BiopetCommandLineFunction {
@Output
(
doc
=
"Output"
,
shortName
=
"out"
)
var
output
:
File
=
_
execut
e
ble
=
config
(
"exe"
,
"fastqc"
)
execut
a
ble
=
config
(
"exe"
,
"fastqc"
)
var
java_exe
:
String
=
config
(
"exe"
,
"java"
,
"java"
)
var
kmers
:
Int
=
config
(
"kmers"
,
5
)
var
quiet
:
Boolean
=
config
(
"quiet"
,
false
)
...
...
@@ -28,15 +28,15 @@ class Fastqc(val root:Configurable) extends BiopetCommandLineFunction {
override
val
defaultThreads
=
4
override
def
afterGraph
{
this
.
checkExecut
e
ble
val
fastqcDir
=
execut
e
ble
.
substring
(
0
,
execut
e
ble
.
lastIndexOf
(
"/"
))
this
.
checkExecut
a
ble
val
fastqcDir
=
execut
a
ble
.
substring
(
0
,
execut
a
ble
.
lastIndexOf
(
"/"
))
if
(
contaminants
==
null
)
contaminants
=
new
File
(
fastqcDir
+
"/Contaminants/contaminant_list.txt"
)
}
override
def
versionCommand
=
execut
e
ble
+
" --version"
override
def
versionCommand
=
execut
a
ble
+
" --version"
def
cmdLine
=
{
required
(
execut
e
ble
)
+
required
(
execut
a
ble
)
+
optional
(
"--java"
,
java_exe
)
+
optional
(
"--threads"
,
threads
)
+
optional
(
"--contaminants"
,
contaminants
)
+
...
...
flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Sickle.scala
View file @
95ba716f
...
...
@@ -29,7 +29,7 @@ class Sickle(val root:Configurable) extends BiopetCommandLineFunction {
@Output
(
doc
=
"stats output"
)
var
output_stats
:
File
=
null
execut
e
ble
=
config
(
"exe"
,
"sickle"
)
execut
a
ble
=
config
(
"exe"
,
"sickle"
)
var
qualityType
:
String
=
config
(
"qualitytype"
,
null
)
var
defaultQualityType
:
String
=
_
...
...
@@ -40,14 +40,14 @@ class Sickle(val root:Configurable) extends BiopetCommandLineFunction {
if
(
qualityType
==
null
&&
defaultQualityType
!=
null
)
qualityType
=
defaultQualityType
}
override
def
versionCommand
=
execut
e
ble
+
" --version"
override
def
versionCommand
=
execut
a
ble
+
" --version"
override
def
beforeCmd
{
qualityType
=
getQualityTypeFromFile
}
def
cmdLine
=
{
var
cmd
:
String
=
required
(
execut
e
ble
)
var
cmd
:
String
=
required
(
execut
a
ble
)
if
(
input_R2
!=
null
)
{
cmd
+=
required
(
"pe"
)
+
required
(
"-r"
,
input_R2
)
+
...
...
mapping/src/main/scala/nl/lumc/sasc/biopet/function/aligners/Bwa.scala
View file @
95ba716f
...
...
@@ -22,17 +22,17 @@ class Bwa(val root:Configurable) extends BiopetCommandLineFunction {
var
RG
:
String
=
_
var
M
:
Boolean
=
config
(
"M"
,
true
)
execut
e
ble
=
config
(
"exe"
,
"bwa"
)
execut
a
ble
=
config
(
"exe"
,
"bwa"
)
override
val
versionRegex
=
"""Version: (.*)"""
.
r
override
val
versionExitcode
=
List
(
0
,
1
)
override
val
defaultVmem
=
"6G"
override
val
defaultThreads
=
8
override
def
versionCommand
=
execut
e
ble
override
def
versionCommand
=
execut
a
ble
def
cmdLine
=
{
required
(
execut
e
ble
)
+
required
(
execut
a
ble
)
+
required
(
"mem"
)
+
optional
(
"-t"
,
nCoresRequest
)
+
optional
(
"-R"
,
RG
)
+
...
...
mapping/src/main/scala/nl/lumc/sasc/biopet/function/aligners/Star.scala
View file @
95ba716f
...
...
@@ -34,7 +34,7 @@ class Star(val root:Configurable) extends BiopetCommandLineFunction {
@Output
(
doc
=
"Output SAindex file"
,
required
=
false
)
var
outputSAindex
:
File
=
_
execut
e
ble
=
config
(
"exe"
,
"STAR"
)
execut
a
ble
=
config
(
"exe"
,
"STAR"
)
@Argument
(
doc
=
"Output Directory"
)
var
outputDir
:
String
=
_
...
...
@@ -64,7 +64,7 @@ class Star(val root:Configurable) extends BiopetCommandLineFunction {
}
def
cmdLine
:
String
=
{
var
cmd
:
String
=
required
(
"cd"
,
outputDir
)
+
"&&"
+
required
(
execut
e
ble
)
var
cmd
:
String
=
required
(
"cd"
,
outputDir
)
+
"&&"
+
required
(
execut
a
ble
)
if
(
runmode
!=
null
&&
runmode
==
"genomeGenerate"
)
{
// Create index
cmd
+=
required
(
"--runMode"
,
runmode
)
+
required
(
"--genomeFastaFiles"
,
referenceFile
)
...
...
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