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biopet.biopet
Commits
a3af8046
Commit
a3af8046
authored
Jul 03, 2015
by
Peter van 't Hof
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Fix code style warnings
parent
fd956f72
Changes
65
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65 changed files
with
184 additions
and
177 deletions
+184
-177
public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
...c/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
+3
-3
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala
...rc/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala
+3
-4
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cat.scala
...k/src/main/scala/nl/lumc/sasc/biopet/extensions/Cat.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala
.../main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Freebayes.scala
...main/scala/nl/lumc/sasc/biopet/extensions/Freebayes.scala
+4
-2
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Gzip.scala
.../src/main/scala/nl/lumc/sasc/biopet/extensions/Gzip.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Ln.scala
...rk/src/main/scala/nl/lumc/sasc/biopet/extensions/Ln.scala
+7
-7
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Md5sum.scala
...rc/main/scala/nl/lumc/sasc/biopet/extensions/Md5sum.scala
+2
-2
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Pbzip2.scala
...rc/main/scala/nl/lumc/sasc/biopet/extensions/Pbzip2.scala
+3
-3
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/PythonCommandLineFunction.scala
...mc/sasc/biopet/extensions/PythonCommandLineFunction.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala
...src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala
+2
-2
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RscriptCommandLineFunction.scala
...c/sasc/biopet/extensions/RscriptCommandLineFunction.scala
+3
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala
...ain/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala
+2
-2
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Sha1sum.scala
...c/main/scala/nl/lumc/sasc/biopet/extensions/Sha1sum.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala
...rc/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala
+4
-6
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Stampy.scala
...rc/main/scala/nl/lumc/sasc/biopet/extensions/Stampy.scala
+2
-2
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala
.../src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala
+9
-9
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Tabix.scala
...src/main/scala/nl/lumc/sasc/biopet/extensions/Tabix.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala
.../lumc/sasc/biopet/extensions/VariantEffectPredictor.scala
+2
-2
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Zcat.scala
.../src/main/scala/nl/lumc/sasc/biopet/extensions/Zcat.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/BcftoolsCall.scala
...l/lumc/sasc/biopet/extensions/bcftools/BcftoolsCall.scala
+2
-5
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala
...mc/sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsIntersect.scala
...c/sasc/biopet/extensions/bedtools/BedtoolsIntersect.scala
+2
-2
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/Breakdancer.scala
...lumc/sasc/biopet/extensions/breakdancer/Breakdancer.scala
+3
-3
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerCaller.scala
...asc/biopet/extensions/breakdancer/BreakdancerCaller.scala
+2
-2
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerConfig.scala
...asc/biopet/extensions/breakdancer/BreakdancerConfig.scala
+3
-3
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerVCF.scala
...c/sasc/biopet/extensions/breakdancer/BreakdancerVCF.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaAln.scala
...ain/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaAln.scala
+2
-2
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala
...ain/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala
+2
-2
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSampe.scala
...n/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSampe.scala
+2
-2
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSamse.scala
...n/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSamse.scala
+2
-2
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/clever/Clever.scala
.../scala/nl/lumc/sasc/biopet/extensions/clever/Clever.scala
+3
-3
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/clever/CleverCaller.scala
.../nl/lumc/sasc/biopet/extensions/clever/CleverCaller.scala
+3
-3
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/delly/Delly.scala
...in/scala/nl/lumc/sasc/biopet/extensions/delly/Delly.scala
+3
-3
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CombineVariants.scala
...nl/lumc/sasc/biopet/extensions/gatk/CombineVariants.scala
+4
-2
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/Gatk.scala
...main/scala/nl/lumc/sasc/biopet/extensions/gatk/Gatk.scala
+4
-2
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVTools.scala
...la/nl/lumc/sasc/biopet/extensions/igvtools/IGVTools.scala
+5
-4
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVToolsCount.scala
.../lumc/sasc/biopet/extensions/igvtools/IGVToolsCount.scala
+6
-6
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/kraken/Kraken.scala
.../scala/nl/lumc/sasc/biopet/extensions/kraken/Kraken.scala
+3
-3
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2CallPeak.scala
.../nl/lumc/sasc/biopet/extensions/macs2/Macs2CallPeak.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/AddOrReplaceReadGroups.scala
...asc/biopet/extensions/picard/AddOrReplaceReadGroups.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/BedToIntervalList.scala
...umc/sasc/biopet/extensions/picard/BedToIntervalList.scala
+2
-0
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CalculateHsMetrics.scala
...mc/sasc/biopet/extensions/picard/CalculateHsMetrics.scala
+2
-2
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetrics.scala
...et/extensions/picard/CollectAlignmentSummaryMetrics.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala
.../sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala
+3
-3
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetrics.scala
...c/biopet/extensions/picard/CollectInsertSizeMetrics.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectMultipleMetrics.scala
...asc/biopet/extensions/picard/CollectMultipleMetrics.scala
+12
-15
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectRnaSeqMetrics.scala
.../sasc/biopet/extensions/picard/CollectRnaSeqMetrics.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectTargetedPcrMetrics.scala
.../biopet/extensions/picard/CollectTargetedPcrMetrics.scala
+4
-2
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectWgsMetrics.scala
...umc/sasc/biopet/extensions/picard/CollectWgsMetrics.scala
+4
-2
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala
...l/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala
+2
-2
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala
.../scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala
+5
-8
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/ReorderSam.scala
...la/nl/lumc/sasc/biopet/extensions/picard/ReorderSam.scala
+2
-2
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SortSam.scala
...scala/nl/lumc/sasc/biopet/extensions/picard/SortSam.scala
+3
-3
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/Pindel.scala
.../scala/nl/lumc/sasc/biopet/extensions/pindel/Pindel.scala
+3
-3
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelCaller.scala
.../nl/lumc/sasc/biopet/extensions/pindel/PindelCaller.scala
+2
-2
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelConfig.scala
.../nl/lumc/sasc/biopet/extensions/pindel/PindelConfig.scala
+9
-9
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/rscript/LinePlot.scala
...ala/nl/lumc/sasc/biopet/extensions/rscript/LinePlot.scala
+3
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/rscript/StackedBarPlot.scala
.../lumc/sasc/biopet/extensions/rscript/StackedBarPlot.scala
+2
-0
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaIndex.scala
.../lumc/sasc/biopet/extensions/sambamba/SambambaIndex.scala
+3
-3
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaMarkdup.scala
...umc/sasc/biopet/extensions/sambamba/SambambaMarkdup.scala
+2
-2
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsMpileup.scala
...umc/sasc/biopet/extensions/samtools/SamtoolsMpileup.scala
+5
-5
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsView.scala
...l/lumc/sasc/biopet/extensions/samtools/SamtoolsView.scala
+3
-3
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/seqtk/SeqtkSeq.scala
...scala/nl/lumc/sasc/biopet/extensions/seqtk/SeqtkSeq.scala
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/Mpileup2cns.scala
.../nl/lumc/sasc/biopet/extensions/varscan/Mpileup2cns.scala
+1
-1
No files found.
public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
View file @
a3af8046
...
...
@@ -5,7 +5,7 @@ import java.io.{ File, PrintWriter }
import
nl.lumc.sasc.biopet.core.config.Configurable
import
nl.lumc.sasc.biopet.core.report.
{
ReportBuilderExtension
,
ReportBuilder
,
ReportPage
,
ReportSection
}
import
nl.lumc.sasc.biopet.core.summary.
{
Summary
,
SummaryValue
}
import
nl.lumc.sasc.biopet.extensions.rscript.
{
StackedBarPlot
,
XY
Plot
}
import
nl.lumc.sasc.biopet.extensions.rscript.
{
StackedBarPlot
,
Line
Plot
}
class
BammetricsReport
(
val
root
:
Configurable
)
extends
ReportBuilderExtension
{
val
builder
=
BammetricsReport
...
...
@@ -204,7 +204,7 @@ object BammetricsReport extends ReportBuilder {
tsvWriter
.
close
()
val
plot
=
new
XY
Plot
(
null
)
val
plot
=
new
Line
Plot
(
null
)
plot
.
input
=
tsvFile
plot
.
output
=
pngFile
plot
.
ylabel
=
Some
(
"Reads"
)
...
...
@@ -292,7 +292,7 @@ object BammetricsReport extends ReportBuilder {
tsvWriter
.
close
()
val
plot
=
new
XY
Plot
(
null
)
val
plot
=
new
Line
Plot
(
null
)
plot
.
input
=
tsvFile
plot
.
output
=
pngFile
plot
.
ylabel
=
Some
(
"Bases"
)
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala
View file @
a3af8046
...
...
@@ -59,8 +59,8 @@ class Bowtie(val root: Configurable) extends BiopetCommandLineFunction with Refe
var
maqerr
:
Option
[
Int
]
=
config
(
"maqerr"
)
var
maxins
:
Option
[
Int
]
=
config
(
"maxins"
)
override
def
beforeGraph
{
super
.
beforeGraph
override
def
beforeGraph
()
{
super
.
beforeGraph
()
if
(
reference
==
null
)
reference
=
referenceFasta
()
}
...
...
@@ -81,10 +81,9 @@ class Bowtie(val root: Configurable) extends BiopetCommandLineFunction with Refe
optional
(
"--maxins"
,
maxins
)
+
required
(
reference
)
+
(
R2
match
{
case
Some
(
r2
)
=>
{
case
Some
(
r2
)
=>
required
(
"-1"
,
R1
)
+
optional
(
"-2"
,
r2
)
}
case
_
=>
required
(
R1
)
})
+
" > "
+
required
(
output
)
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cat.scala
View file @
a3af8046
...
...
@@ -52,6 +52,6 @@ object Cat {
val
cat
=
new
Cat
(
root
)
cat
.
input
=
input
cat
.
output
=
output
return
cat
cat
}
}
\ No newline at end of file
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala
View file @
a3af8046
...
...
@@ -76,7 +76,7 @@ class Cutadapt(val root: Configurable) extends BiopetCommandLineFunction with Su
val
stats
:
mutable.Map
[
String
,
Int
]
=
mutable
.
Map
(
"trimmed"
->
0
,
"tooshort"
->
0
,
"toolong"
->
0
)
val
adapter_stats
:
mutable.Map
[
String
,
Int
]
=
mutable
.
Map
()
if
(
stats_output
.
exists
)
for
(
line
<-
Source
.
fromFile
(
stats_output
).
getLines
)
{
if
(
stats_output
.
exists
)
for
(
line
<-
Source
.
fromFile
(
stats_output
).
getLines
()
)
{
line
match
{
case
trimR
(
m
)
=>
stats
+=
(
"trimmed"
->
m
.
toInt
)
case
tooShortR
(
m
)
=>
stats
+=
(
"tooshort"
->
m
.
toInt
)
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Freebayes.scala
View file @
a3af8046
...
...
@@ -22,6 +22,8 @@ import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunction, Reference }
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
/**
* Extension for freebayes
*
* Created by pjvan_thof on 3/3/15.
*/
class
Freebayes
(
val
root
:
Configurable
)
extends
BiopetCommandLineFunction
with
Reference
{
...
...
@@ -42,8 +44,8 @@ class Freebayes(val root: Configurable) extends BiopetCommandLineFunction with R
override
val
versionRegex
=
"""version: (.*)"""
.
r
override
def
versionCommand
=
executable
+
" --version"
override
def
beforeGraph
:
Unit
=
{
super
.
beforeGraph
override
def
beforeGraph
()
:
Unit
=
{
super
.
beforeGraph
()
reference
=
referenceFasta
()
}
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Gzip.scala
View file @
a3af8046
...
...
@@ -41,6 +41,6 @@ object Gzip {
val
gzip
=
new
Gzip
(
root
)
gzip
.
input
=
input
gzip
.
output
=
output
return
gzip
gzip
}
}
\ No newline at end of file
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Ln.scala
View file @
a3af8046
...
...
@@ -51,11 +51,11 @@ class Ln(val root: Configurable) extends InProcessFunction with Configurable {
lazy
val
cmd
:
String
=
{
lazy
val
inCanonical
:
String
=
{
// need to remove "/~" to correctly expand path with tilde
input
.
getCanonicalPath
()
.
replace
(
"/~"
,
""
)
input
.
getCanonicalPath
.
replace
(
"/~"
,
""
)
}
lazy
val
outCanonical
:
String
=
{
output
.
getCanonicalPath
()
.
replace
(
"/~"
,
""
)
output
.
getCanonicalPath
.
replace
(
"/~"
,
""
)
}
lazy
val
inToks
:
Array
[
String
]
=
{
...
...
@@ -68,8 +68,8 @@ class Ln(val root: Configurable) extends InProcessFunction with Configurable {
lazy
val
commonPrefixLength
:
Int
=
{
val
maxLength
=
scala
.
math
.
min
(
inToks
.
length
,
outToks
.
length
)
var
i
:
Int
=
0
;
while
(
i
<
maxLength
&&
inToks
(
i
)
==
outToks
(
i
))
i
+=
1
;
var
i
:
Int
=
0
while
(
i
<
maxLength
&&
inToks
(
i
)
==
outToks
(
i
))
i
+=
1
i
}
...
...
@@ -108,11 +108,11 @@ class Ln(val root: Configurable) extends InProcessFunction with Configurable {
}
}
override
def
run
{
override
def
run
()
{
val
stdout
=
new
StringBuffer
()
val
stderr
=
new
StringBuffer
()
val
process
=
Process
(
cmd
).
run
(
ProcessLogger
(
stdout
append
_
+
"\n"
,
stderr
append
_
+
"\n"
))
val
exitcode
=
process
.
exitValue
val
exitcode
=
process
.
exitValue
()
if
(
exitcode
!=
0
)
{
throw
new
Exception
(
"Error creating symbolic link, this was the original message: \n"
+
stderr
)
}
...
...
@@ -136,6 +136,6 @@ object Ln {
ln
.
input
=
input
ln
.
output
=
output
ln
.
relative
=
relative
return
ln
ln
}
}
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Md5sum.scala
View file @
a3af8046
...
...
@@ -45,7 +45,7 @@ object Md5sum {
val
md5sum
=
new
Md5sum
(
root
)
md5sum
.
input
=
fastqfile
md5sum
.
output
=
new
File
(
outDir
,
fastqfile
.
getName
+
".md5"
)
return
md5sum
md5sum
}
/** Makes md5sum with md5 file in same dir as input file */
...
...
@@ -53,6 +53,6 @@ object Md5sum {
val
md5sum
=
new
Md5sum
(
root
)
md5sum
.
input
=
file
md5sum
.
output
=
new
File
(
file
.
getParentFile
,
file
.
getName
+
".md5"
)
return
md5sum
md5sum
}
}
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Pbzip2.scala
View file @
a3af8046
...
...
@@ -37,8 +37,8 @@ class Pbzip2(val root: Configurable) extends BiopetCommandLineFunction {
override
val
defaultCoreMemory
=
memory
.
getOrElse
(
1000
).
toDouble
/
1000
override
val
defaultThreads
=
2
override
def
beforeCmd
{
if
(
!
memory
.
isEmpty
)
memory
=
Option
(
memory
.
get
*
threads
)
override
def
beforeCmd
()
{
if
(
memory
.
isDefined
)
memory
=
Option
(
memory
.
get
*
threads
)
}
/** return commandline to execute */
...
...
@@ -58,6 +58,6 @@ object Pbzip2 {
val
pbzip2
=
new
Pbzip2
(
root
)
pbzip2
.
input
=
input
pbzip2
.
output
=
output
return
pbzip2
pbzip2
}
}
\ No newline at end of file
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/PythonCommandLineFunction.scala
View file @
a3af8046
...
...
@@ -57,7 +57,7 @@ trait PythonCommandLineFunction extends BiopetCommandLineFunction {
}
/** return basic command to prefix the complete command with */
def
getPythonCommand
()
:
String
=
{
def
getPythonCommand
:
String
=
{
required
(
executable
)
+
required
(
python_script
)
}
}
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala
View file @
a3af8046
...
...
@@ -72,11 +72,11 @@ class Raxml(val root: Configurable) extends BiopetCommandLineFunction {
var
executableThreads
:
Option
[
String
]
=
config
(
"exe_pthreads"
)
/** Sets correct output files to job */
override
def
beforeGraph
{
override
def
beforeGraph
()
{
require
(
w
!=
null
)
if
(
threads
==
0
)
threads
=
getThreads
(
defaultThreads
)
executable
=
if
(
threads
>
1
&&
executableThreads
.
isDefined
)
executableThreads
.
get
else
executableNonThreads
super
.
beforeGraph
super
.
beforeGraph
()
out
:::=
List
(
Some
(
getInfoFile
),
getBestTreeFile
,
getBootstrapFile
,
getBipartitionsFile
).
flatten
f
match
{
case
"d"
if
b
.
isEmpty
=>
for
(
t
<-
0
until
N
.
getOrElse
(
1
))
{
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RscriptCommandLineFunction.scala
View file @
a3af8046
...
...
@@ -22,6 +22,8 @@ import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import
scala.sys.process._
/**
* General rscript extension
*
* Created by wyleung on 17-2-15.
*/
trait
RscriptCommandLineFunction
extends
BiopetCommandLineFunction
{
...
...
@@ -30,7 +32,7 @@ trait RscriptCommandLineFunction extends BiopetCommandLineFunction {
executable
=
config
(
"exe"
,
default
=
"Rscript"
,
submodule
=
"Rscript"
)
override
def
beforeGraph
:
Unit
=
{
override
def
beforeGraph
()
:
Unit
=
{
checkScript
()
}
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala
View file @
a3af8046
...
...
@@ -53,8 +53,8 @@ class RunGubbins(val root: Configurable) extends BiopetCommandLineFunction {
var
noCleanup
:
Boolean
=
config
(
"no_cleanup"
,
default
=
false
)
/** Set correct output files */
override
def
beforeGraph
:
Unit
=
{
super
.
beforeGraph
override
def
beforeGraph
()
:
Unit
=
{
super
.
beforeGraph
()
require
(
outputDirectory
!=
null
)
jobLocalDir
=
outputDirectory
if
(
prefix
.
isEmpty
)
prefix
=
Some
(
fastafile
.
getName
)
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Sha1sum.scala
View file @
a3af8046
...
...
@@ -41,6 +41,6 @@ object Sha1sum {
val
sha1sum
=
new
Sha1sum
(
root
)
sha1sum
.
input
=
input
sha1sum
.
output
=
new
File
(
outDir
,
input
.
getName
+
".sha1"
)
return
sha1sum
sha1sum
}
}
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala
View file @
a3af8046
...
...
@@ -62,7 +62,7 @@ class Sickle(val root: Configurable) extends BiopetCommandLineFunction with Summ
override
def
versionCommand
=
executable
+
" --version"
/** Sets qualityType is still empty */
override
def
beforeGraph
{
override
def
beforeGraph
()
{
if
(
qualityType
.
isEmpty
)
qualityType
=
Some
(
defaultQualityType
)
}
...
...
@@ -100,22 +100,20 @@ class Sickle(val root: Configurable) extends BiopetCommandLineFunction with Summ
var
stats
:
mutable.Map
[
String
,
Int
]
=
mutable
.
Map
()
if
(
output_stats
.
exists
)
for
(
line
<-
Source
.
fromFile
(
output_stats
).
getLines
)
{
if
(
output_stats
.
exists
)
for
(
line
<-
Source
.
fromFile
(
output_stats
).
getLines
()
)
{
line
match
{
// single run
case
sKept
(
num
)
=>
stats
+=
(
"num_reads_kept"
->
num
.
toInt
)
case
sDiscarded
(
num
)
=>
stats
+=
(
"num_reads_discarded_total"
->
num
.
toInt
)
// paired run
case
pPairKept
(
reads
,
pairs
)
=>
stats
+=
(
"num_reads_kept"
->
reads
.
toInt
)
case
pSingleKept
(
total
,
r1
,
r2
)
=>
{
case
pSingleKept
(
total
,
r1
,
r2
)
=>
stats
+=
(
"num_reads_kept_R1"
->
r1
.
toInt
)
stats
+=
(
"num_reads_kept_R2"
->
r2
.
toInt
)
}
case
pPairDiscarded
(
reads
,
pairs
)
=>
stats
+=
(
"num_reads_discarded_both"
->
reads
.
toInt
)
case
pSingleDiscarded
(
total
,
r1
,
r2
)
=>
{
case
pSingleDiscarded
(
total
,
r1
,
r2
)
=>
stats
+=
(
"num_reads_discarded_R1"
->
r1
.
toInt
)
stats
+=
(
"num_reads_discarded_R2"
->
r2
.
toInt
)
}
case
_
=>
}
}
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Stampy.scala
View file @
a3af8046
...
...
@@ -70,8 +70,8 @@ class Stampy(val root: Configurable) extends BiopetCommandLineFunction with Refe
override
def
versionCommand
=
executable
+
" --help"
/** Sets readgroup when not set yet */
override
def
beforeGraph
:
Unit
=
{
super
.
beforeGraph
override
def
beforeGraph
()
:
Unit
=
{
super
.
beforeGraph
()
require
(
readgroup
!=
null
)
if
(
reference
==
null
)
reference
=
referenceFasta
()
}
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala
View file @
a3af8046
...
...
@@ -68,7 +68,7 @@ class Star(val root: Configurable) extends BiopetCommandLineFunction with Refere
/** Sets output files for the graph */
override
def
beforeGraph
()
{
super
.
beforeGraph
super
.
beforeGraph
()
if
(
reference
==
null
)
reference
=
referenceFasta
()
genomeDir
=
config
(
"genomeDir"
,
new
File
(
reference
.
getAbsoluteFile
.
getParent
,
"star"
))
if
(
outFileNamePrefix
!=
null
&&
!
outFileNamePrefix
.
endsWith
(
"."
))
outFileNamePrefix
+=
"."
...
...
@@ -111,7 +111,7 @@ object Star {
* @param R1 R1 fastq file
* @param R2 R2 fastq file
* @param outputDir Outputdir for Star
* @param isIntermediate
* @param isIntermediate
When set true jobs are flaged as intermediate
* @param deps Deps to add to wait on run
* @return Return Star
*
...
...
@@ -123,8 +123,8 @@ object Star {
star
.
outputDir
=
outputDir
star
.
isIntermediate
=
isIntermediate
star
.
deps
=
deps
star
.
beforeGraph
return
star
star
.
beforeGraph
()
star
}
/**
...
...
@@ -133,7 +133,7 @@ object Star {
* @param R1 R1 fastq file
* @param R2 R2 fastq file
* @param outputDir Outputdir for Star
* @param isIntermediate
* @param isIntermediate
When set true jobs are flaged as intermediate
* @param deps Deps to add to wait on run
* @return Return Star
*/
...
...
@@ -146,21 +146,21 @@ object Star {
val
starCommand_pass1
=
Star
(
configurable
,
R1
,
R2
,
new
File
(
outputDir
,
"aln-pass1"
))
starCommand_pass1
.
isIntermediate
=
isIntermediate
starCommand_pass1
.
deps
=
deps
starCommand_pass1
.
beforeGraph
starCommand_pass1
.
beforeGraph
()
val
starCommand_reindex
=
new
Star
(
configurable
)
starCommand_reindex
.
sjdbFileChrStartEnd
=
starCommand_pass1
.
outputTab
starCommand_reindex
.
outputDir
=
new
File
(
outputDir
,
"re-index"
)
starCommand_reindex
.
runmode
=
"genomeGenerate"
starCommand_reindex
.
isIntermediate
=
isIntermediate
starCommand_reindex
.
beforeGraph
starCommand_reindex
.
beforeGraph
()
val
starCommand_pass2
=
Star
(
configurable
,
R1
,
R2
,
new
File
(
outputDir
,
"aln-pass2"
))
starCommand_pass2
.
genomeDir
=
starCommand_reindex
.
outputDir
starCommand_pass2
.
isIntermediate
=
isIntermediate
starCommand_pass2
.
deps
=
deps
starCommand_pass2
.
beforeGraph
starCommand_pass2
.
beforeGraph
()
return
(
starCommand_pass2
.
outputSam
,
List
(
starCommand_pass1
,
starCommand_reindex
,
starCommand_pass2
))
(
starCommand_pass2
.
outputSam
,
List
(
starCommand_pass1
,
starCommand_reindex
,
starCommand_pass2
))
}
}
\ No newline at end of file
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Tabix.scala
View file @
a3af8046
...
...
@@ -66,7 +66,7 @@ class Tabix(val root: Configurable) extends BiopetCommandLineFunction {
/** Formats that tabix can handle */
private
val
validFormats
:
Set
[
String
]
=
Set
(
"gff"
,
"bed"
,
"sam"
,
"vcf"
,
"psltbl"
)
override
def
beforeGraph
:
Unit
=
{
override
def
beforeGraph
()
:
Unit
=
{
p
match
{
case
Some
(
fmt
)
=>
require
(
validFormats
.
contains
(
fmt
),
"-p flag must be one of "
+
validFormats
.
mkString
(
", "
))
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala
View file @
a3af8046
...
...
@@ -141,8 +141,8 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
var
db_version
:
Option
[
Int
]
=
config
(
"db_version"
)
var
buffer_size
:
Option
[
Int
]
=
config
(
"buffer_size"
)
override
def
beforeGraph
:
Unit
=
{
super
.
beforeGraph
override
def
beforeGraph
()
:
Unit
=
{
super
.
beforeGraph
()
if
(!
cache
&&
!
database
)
{
throw
new
IllegalArgumentException
(
"Must supply either cache or database"
)
}
else
if
(
cache
&&
dir
.
isEmpty
)
{
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Zcat.scala
View file @
a3af8046
...
...
@@ -44,6 +44,6 @@ object Zcat {
val
zcat
=
new
Zcat
(
root
)
zcat
.
input
=
input
zcat
.
output
=
output
return
zcat
zcat
}
}
\ No newline at end of file
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/BcftoolsCall.scala
View file @
a3af8046
...
...
@@ -20,10 +20,7 @@ import java.io.File
import
nl.lumc.sasc.biopet.core.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
/**
* This extension is based on bcftools 1.1-134
* @param root
*/
/** This extension is based on bcftools 1.1-134 */
class
BcftoolsCall
(
val
root
:
Configurable
)
extends
Bcftools
{
@Input
(
doc
=
"Input File"
)
var
input
:
File
=
_
...
...
@@ -36,7 +33,7 @@ class BcftoolsCall(val root: Configurable) extends Bcftools {
var
c
:
Boolean
=
config
(
"c"
,
default
=
false
)
var
m
:
Boolean
=
config
(
"m"
,
default
=
false
)
override
def
beforeGraph
:
Unit
=
{
override
def
beforeGraph
()
:
Unit
=
{
require
(
c
!=
m
)
}
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala
View file @
a3af8046
...
...
@@ -43,7 +43,7 @@ class BedtoolsCoverage(val root: Configurable) extends Bedtools {
var
inputTag
=
"-a"
override
def
beforeCmd
{
override
def
beforeCmd
()
{
if
(
input
.
getName
.
endsWith
(
".bam"
))
inputTag
=
"-abam"
}
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsIntersect.scala
View file @
a3af8046
...
...
@@ -40,7 +40,7 @@ class BedtoolsIntersect(val root: Configurable) extends Bedtools {
var
inputTag
=
"-a"
override
def
beforeCmd
{
override
def
beforeCmd
()
{
if
(
input
.
getName
.
endsWith
(
".bam"
))
inputTag
=
"-abam"
}
...
...
@@ -63,6 +63,6 @@ object BedtoolsIntersect {
bedtoolsIntersect
.
output
=
output
bedtoolsIntersect
.
minOverlap
=
minOverlap
bedtoolsIntersect
.
count
=
count
return
bedtoolsIntersect
bedtoolsIntersect
}
}
\ No newline at end of file
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/Breakdancer.scala
View file @
a3af8046
...
...
@@ -77,8 +77,8 @@ object Breakdancer extends PipelineCommand {
breakdancer
.
input
=
input
breakdancer
.
reference
=
reference
breakdancer
.
workdir
=
runDir
breakdancer
.
init
breakdancer
.
biopetScript
return
breakdancer
breakdancer
.
init
()
breakdancer
.
biopetScript
()
breakdancer
}
}
\ No newline at end of file
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerCaller.scala
View file @
a3af8046
...
...
@@ -58,7 +58,7 @@ class BreakdancerCaller(val root: Configurable) extends BiopetCommandLineFunctio
var
h
:
Boolean
=
config
(
"h"
,
default
=
false
)
var
y
:
Option
[
Int
]
=
config
(
"y"
,
default
=
30
)
override
def
beforeCmd
{
override
def
beforeCmd
()
{
}
def
cmdLine
=
required
(
executable
)
+
...
...
@@ -86,6 +86,6 @@ object BreakdancerCaller {
val
bdcaller
=
new
BreakdancerCaller
(
root
)
bdcaller
.
input
=
input
bdcaller
.
output
=
output
return
bdcaller
bdcaller
}
}
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerConfig.scala
View file @
a3af8046
...
...
@@ -43,17 +43,17 @@ object BreakdancerConfig {
val
bdconf
=
new
BreakdancerConfig
(
root
)
bdconf
.
input
=
input
bdconf
.
output
=
output
return
bdconf
bdconf
}
def
apply
(
root
:
Configurable
,
input
:
File
,
outputDir
:
String
)
:
BreakdancerConfig
=
{
val
dir
=
if
(
outputDir
.
endsWith
(
"/"
))
outputDir
else
outputDir
+
"/"
val
outputFile
=
new
File
(
dir
+
swapExtension
(
input
.
getName
))
return
apply
(
root
,
input
,
outputFile
)
apply
(
root
,
input
,
outputFile
)
}
def
apply
(
root
:
Configurable
,
input
:
File
)
:
BreakdancerConfig
=
{
return
apply
(
root
,
input
,
new
File
(
swapExtension
(
input
.
getAbsolutePath
)))
apply
(
root
,
input
,
new
File
(
swapExtension
(
input
.
getAbsolutePath
)))
}
private
def
swapExtension
(
inputFile
:
String
)
=
inputFile
.
substring
(
0
,
inputFile
.
lastIndexOf
(
".bam"
))
+
".breakdancer.cfg"
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerVCF.scala
View file @
a3af8046
...
...
@@ -42,6 +42,6 @@ object BreakdancerVCF {
val
bd
=
new
BreakdancerVCF
(
root
)
bd
.
input
=
input
bd
.
output
=
output
return
bd
bd
}
}
\ No newline at end of file
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaAln.scala
View file @
a3af8046
...
...
@@ -64,8 +64,8 @@ class BwaAln(val root: Configurable) extends Bwa with Reference {
override
val
defaultCoreMemory
=
4.0
override
val
defaultThreads
=
8
override
def
beforeGraph
{
super
.
beforeGraph
override
def
beforeGraph
()
{
super
.
beforeGraph
()
if
(
reference
==
null
)
reference
=
referenceFasta
()
}
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala
View file @
a3af8046
...
...
@@ -71,8 +71,8 @@ class BwaMem(val root: Configurable) extends Bwa with Reference {
override
val
defaultCoreMemory
=
4.0
override
val
defaultThreads
=
8
override
def
beforeGraph
{
super
.
beforeGraph
override
def
beforeGraph
()
{
super
.
beforeGraph
()
if
(
reference
==
null
)
reference
=
referenceFasta
()
}
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSampe.scala
View file @
a3af8046
...
...
@@ -57,8 +57,8 @@ class BwaSampe(val root: Configurable) extends Bwa with Reference {
var
r
:
String
=
_
override
def
beforeGraph
{
super
.
beforeGraph
override
def
beforeGraph
()
{
super
.
beforeGraph
()
if
(
reference
==
null
)
reference
=
referenceFasta
()
}
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSamse.scala
View file @
a3af8046
...
...
@@ -43,8 +43,8 @@ class BwaSamse(val root: Configurable) extends Bwa with Reference {
var
n
:
Option
[
Int
]
=
config
(
"n"
)
var
r
:
String
=
_
override
def
beforeGraph
{
super
.
beforeGraph
override
def
beforeGraph
()
{
super
.
beforeGraph
()
if
(
reference
==
null
)
reference
=
referenceFasta
()
}
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/clever/Clever.scala
View file @
a3af8046
...
...
@@ -57,9 +57,9 @@ object Clever extends PipelineCommand {
val
cleverpipeline
=
new
Clever
(
root
)