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Mirrors
biopet.biopet
Commits
00a24e74
Commit
00a24e74
authored
Mar 15, 2016
by
Peter van 't Hof
Browse files
Fix missing name refactorings
parent
c2ef1e2e
Changes
10
Hide whitespace changes
Inline
Side-by-side
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala
View file @
00a24e74
...
...
@@ -265,8 +265,8 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
def
summaryStats
:
Map
[
String
,
Any
]
=
{
if
(
statsText
)
{
val
stats
_f
ile
:
File
=
new
File
(
output
.
getAbsolutePath
+
"_summary.txt"
)
parseStatsFile
(
stats
_f
ile
)
val
stats
F
ile
:
File
=
new
File
(
output
.
getAbsolutePath
+
"_summary.txt"
)
parseStatsFile
(
stats
F
ile
)
}
else
{
Map
()
}
...
...
public/biopet-tools-extensions/src/test/scala/VcfFilterTest.scala
View file @
00a24e74
...
...
@@ -102,85 +102,45 @@ class VcfFilterTest extends TestNGSuite with Matchers {
val
command
=
cmd
(
vcfFilter
.
cmdLine
)
var
cmdString
:
List
[
String
]
=
Nil
if
(
minSampleDepth
.
isDefined
)
{
cmdString
=
"--minSampleDepth "
+
minSampleDepth
.
getOrElse
(
""
)
::
cmdString
}
if
(
minSampleDepth
.
isDefined
)
cmdString
=
"--minSampleDepth "
+
minSampleDepth
.
getOrElse
(
""
)
::
cmdString
if
(
minTotalDepth
.
isDefined
)
{
cmdString
=
"--minTotalDepth "
+
minTotalDepth
.
getOrElse
(
""
)
::
cmdString
}
if
(
minTotalDepth
.
isDefined
)
cmdString
=
"--minTotalDepth "
+
minTotalDepth
.
getOrElse
(
""
)
::
cmdString
if
(
minAlternateDepth
.
isDefined
)
{
cmdString
=
"--minAlternateDepth "
+
minAlternateDepth
.
getOrElse
(
""
)
::
cmdString
}
if
(
minAlternateDepth
.
isDefined
)
cmdString
=
"--minAlternateDepth "
+
minAlternateDepth
.
getOrElse
(
""
)
::
cmdString
if
(
minSamplesPass
.
isDefined
)
{
cmdString
=
"--minSamplesPass "
+
minSamplesPass
.
getOrElse
(
""
)
::
cmdString
}
if
(
minSamplesPass
.
isDefined
)
cmdString
=
"--minSamplesPass "
+
minSamplesPass
.
getOrElse
(
""
)
::
cmdString
if
(
minGenomeQuality
.
isDefined
)
{
cmdString
=
"--minGenomeQuality "
+
minGenomeQuality
.
getOrElse
(
""
)
::
cmdString
}
if
(
minGenomeQuality
.
isDefined
)
cmdString
=
"--minGenomeQuality "
+
minGenomeQuality
.
getOrElse
(
""
)
::
cmdString
if
(
filterRefCalls
)
{
cmdString
=
"--filterRefCalls"
::
cmdString
}
if
(
filterRefCalls
)
cmdString
=
"--filterRefCalls"
::
cmdString
if
(
invertedOutputVcf
.
isDefined
)
{
cmdString
=
"--invertedOutputVcf "
+
invertedOutputVcf
.
getOrElse
(
new
File
(
""
)).
getAbsolutePath
::
cmdString
}
if
(
invertedOutputVcf
.
isDefined
)
cmdString
=
"--invertedOutputVcf "
+
invertedOutputVcf
.
getOrElse
(
new
File
(
""
)).
getAbsolutePath
::
cmdString
if
(
resToDom
.
isDefined
)
{
cmdString
=
"--resToDom "
+
resToDom
.
getOrElse
(
""
)
::
cmdString
}
if
(
resToDom
.
isDefined
)
cmdString
=
"--resToDom "
+
resToDom
.
getOrElse
(
""
)
::
cmdString
if
(
trioCompound
.
isDefined
)
{
cmdString
=
"--trioCompound "
+
trioCompound
.
getOrElse
(
""
)
::
cmdString
}
if
(
trioCompound
.
isDefined
)
cmdString
=
"--trioCompound "
+
trioCompound
.
getOrElse
(
""
)
::
cmdString
if
(
deNovoInSample
.
isDefined
)
{
cmdString
=
"--deNovoInSample "
+
deNovoInSample
.
getOrElse
(
""
)
::
cmdString
}
if
(
deNovoInSample
.
isDefined
)
cmdString
=
"--deNovoInSample "
+
deNovoInSample
.
getOrElse
(
""
)
::
cmdString
if
(
deNovoTrio
.
isDefined
)
{
cmdString
=
"--deNovoTrio "
+
deNovoTrio
.
getOrElse
(
""
)
::
cmdString
}
if
(
deNovoTrio
.
isDefined
)
cmdString
=
"--deNovoTrio "
+
deNovoTrio
.
getOrElse
(
""
)
::
cmdString
if
(
trioLossOfHet
.
isDefined
)
{
cmdString
=
"--trioLossOfHet "
+
trioLossOfHet
.
getOrElse
(
""
)
::
cmdString
}
if
(
trioLossOfHet
.
isDefined
)
cmdString
=
"--trioLossOfHet "
+
trioLossOfHet
.
getOrElse
(
""
)
::
cmdString
if
(
mustHaveVariant
.
nonEmpty
)
{
cmdString
=
mustHaveVariant
.
map
(
x
=>
"--mustHaveVariant "
+
x
)
:::
cmdString
}
if
(
mustHaveVariant
.
nonEmpty
)
cmdString
=
mustHaveVariant
.
map
(
x
=>
"--mustHaveVariant "
+
x
)
:::
cmdString
if
(
calledIn
.
nonEmpty
)
{
cmdString
=
calledIn
.
map
(
x
=>
"--calledIn "
+
x
)
:::
cmdString
}
if
(
calledIn
.
nonEmpty
)
cmdString
=
calledIn
.
map
(
x
=>
"--calledIn "
+
x
)
:::
cmdString
if
(
mustHaveGenotype
.
nonEmpty
)
{
cmdString
=
mustHaveGenotype
.
map
(
x
=>
"--mustHaveGenotype "
+
x
)
:::
cmdString
}
if
(
mustHaveGenotype
.
nonEmpty
)
cmdString
=
mustHaveGenotype
.
map
(
x
=>
"--mustHaveGenotype "
+
x
)
:::
cmdString
if
(
diffGenotype
.
nonEmpty
)
{
cmdString
=
diffGenotype
.
map
(
x
=>
"--diffGenotype "
+
x
)
:::
cmdString
}
if
(
diffGenotype
.
nonEmpty
)
cmdString
=
diffGenotype
.
map
(
x
=>
"--diffGenotype "
+
x
)
:::
cmdString
if
(
filterHetVarToHomVar
.
nonEmpty
)
{
cmdString
=
filterHetVarToHomVar
.
map
(
x
=>
"--filterHetVarToHomVar "
+
x
)
:::
cmdString
}
if
(
filterHetVarToHomVar
.
nonEmpty
)
cmdString
=
filterHetVarToHomVar
.
map
(
x
=>
"--filterHetVarToHomVar "
+
x
)
:::
cmdString
if
(
id
.
nonEmpty
)
{
cmdString
=
id
.
map
(
x
=>
"--id "
+
x
)
:::
cmdString
}
if
(
id
.
nonEmpty
)
cmdString
=
id
.
map
(
x
=>
"--id "
+
x
)
:::
cmdString
if
(
idFile
.
isDefined
)
{
cmdString
=
"--idFile "
+
idFile
.
getOrElse
(
new
File
(
""
)).
getAbsolutePath
::
cmdString
}
if
(
idFile
.
isDefined
)
cmdString
=
"--idFile "
+
idFile
.
getOrElse
(
new
File
(
""
)).
getAbsolutePath
::
cmdString
if
(
minQualScore
.
isDefined
)
{
cmdString
=
"--minQualScore "
+
minQualScore
.
getOrElse
(
""
)
::
cmdString
}
if
(
minQualScore
.
isDefined
)
cmdString
=
"--minQualScore "
+
minQualScore
.
getOrElse
(
""
)
::
cmdString
cmdString
.
foreach
(
x
=>
command
.
contains
(
x
)
shouldBe
true
)
}
...
...
public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/AnnotateVcfWithBedTest.scala
View file @
00a24e74
...
...
@@ -34,25 +34,25 @@ class AnnotateVcfWithBedTest extends TestNGSuite with MockitoSugar with Matchers
Paths
.
get
(
getClass
.
getResource
(
p
).
toURI
).
toString
}
val
vepped
_p
ath
=
resourcePath
(
"/VEP_oneline.vcf"
)
val
vepped
P
ath
=
resourcePath
(
"/VEP_oneline.vcf"
)
val
bed
=
resourcePath
(
"/rrna01.bed"
)
val
rand
=
new
Random
()
@Test
def
testOutputTypeVcf
()
=
{
val
tmpPath
=
"/tmp/VcfFilter_"
+
rand
.
nextString
(
10
)
+
".vcf"
val
arguments
:
Array
[
String
]
=
Array
(
"-I"
,
vepped
_p
ath
,
"-o"
,
tmpPath
,
"-B"
,
bed
,
"-f"
,
"testing"
)
val
arguments
:
Array
[
String
]
=
Array
(
"-I"
,
vepped
P
ath
,
"-o"
,
tmpPath
,
"-B"
,
bed
,
"-f"
,
"testing"
)
main
(
arguments
)
}
@Test
def
testOutputTypeBcf
()
=
{
val
tmpPath
=
"/tmp/VcfFilter_"
+
rand
.
nextString
(
10
)
+
".bcf"
val
arguments
:
Array
[
String
]
=
Array
(
"-I"
,
vepped
_p
ath
,
"-o"
,
tmpPath
,
"-B"
,
bed
,
"-f"
,
"testing"
)
val
arguments
:
Array
[
String
]
=
Array
(
"-I"
,
vepped
P
ath
,
"-o"
,
tmpPath
,
"-B"
,
bed
,
"-f"
,
"testing"
)
main
(
arguments
)
}
@Test
def
testOutputTypeVcfGz
()
=
{
val
tmpPath
=
"/tmp/VcfFilter_"
+
rand
.
nextString
(
10
)
+
".vcf.gz"
val
arguments
:
Array
[
String
]
=
Array
(
"-I"
,
vepped
_p
ath
,
"-o"
,
tmpPath
,
"-B"
,
bed
,
"-f"
,
"testing"
)
val
arguments
:
Array
[
String
]
=
Array
(
"-I"
,
vepped
P
ath
,
"-o"
,
tmpPath
,
"-B"
,
bed
,
"-f"
,
"testing"
)
main
(
arguments
)
}
...
...
public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/MergeAllelesTest.scala
View file @
00a24e74
...
...
@@ -37,7 +37,7 @@ class MergeAllelesTest extends TestNGSuite with MockitoSugar with Matchers {
Paths
.
get
(
getClass
.
getResource
(
p
).
toURI
).
toString
}
val
vepped
_p
ath
=
resourcePath
(
"/chrQ.vcf.gz"
)
val
vepped
P
ath
=
resourcePath
(
"/chrQ.vcf.gz"
)
val
reference
=
resourcePath
(
"/fake_chrQ.fa"
)
// These two have to created
...
...
@@ -52,7 +52,7 @@ class MergeAllelesTest extends TestNGSuite with MockitoSugar with Matchers {
val
tmp
=
File
.
createTempFile
(
"MergeAlleles"
,
".vcf"
)
tmp
.
deleteOnExit
()
val
tmpPath
=
tmp
.
getAbsolutePath
val
arguments
=
Array
(
"-I"
,
vepped
_p
ath
,
"-o"
,
tmpPath
,
"-R"
,
reference
)
val
arguments
=
Array
(
"-I"
,
vepped
P
ath
,
"-o"
,
tmpPath
,
"-R"
,
reference
)
main
(
arguments
)
}
...
...
@@ -60,7 +60,7 @@ class MergeAllelesTest extends TestNGSuite with MockitoSugar with Matchers {
val
tmp
=
File
.
createTempFile
(
"MergeAlleles"
,
".vcf.gz"
)
tmp
.
deleteOnExit
()
val
tmpPath
=
tmp
.
getAbsolutePath
val
arguments
=
Array
(
"-I"
,
vepped
_p
ath
,
"-o"
,
tmpPath
,
"-R"
,
reference
)
val
arguments
=
Array
(
"-I"
,
vepped
P
ath
,
"-o"
,
tmpPath
,
"-R"
,
reference
)
main
(
arguments
)
}
...
...
@@ -68,7 +68,7 @@ class MergeAllelesTest extends TestNGSuite with MockitoSugar with Matchers {
val
tmp
=
File
.
createTempFile
(
"MergeAlleles"
,
".bcf"
)
tmp
.
deleteOnExit
()
val
tmpPath
=
tmp
.
getAbsolutePath
val
arguments
=
Array
(
"-I"
,
vepped
_p
ath
,
"-o"
,
tmpPath
,
"-R"
,
reference
)
val
arguments
=
Array
(
"-I"
,
vepped
P
ath
,
"-o"
,
tmpPath
,
"-R"
,
reference
)
main
(
arguments
)
}
}
public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VcfFilterTest.scala
View file @
00a24e74
...
...
@@ -39,31 +39,31 @@ class VcfFilterTest extends TestNGSuite with MockitoSugar with Matchers {
Paths
.
get
(
getClass
.
getResource
(
p
).
toURI
).
toString
}
val
vepped
_p
ath
=
resourcePath
(
"/VEP_oneline.vcf"
)
val
vepped
=
new
File
(
vepped
_p
ath
)
val
vepped
P
ath
=
resourcePath
(
"/VEP_oneline.vcf"
)
val
vepped
=
new
File
(
vepped
P
ath
)
val
rand
=
new
Random
()
@Test
def
testOutputTypeVcf
()
=
{
val
tmp
=
File
.
createTempFile
(
"VcfFilter"
,
".vcf"
)
tmp
.
deleteOnExit
()
val
tmp
_p
ath
=
tmp
.
getAbsolutePath
val
arguments
:
Array
[
String
]
=
Array
(
"-I"
,
vepped
_p
ath
,
"-o"
,
tmp
_p
ath
)
val
tmp
P
ath
=
tmp
.
getAbsolutePath
val
arguments
:
Array
[
String
]
=
Array
(
"-I"
,
vepped
P
ath
,
"-o"
,
tmp
P
ath
)
main
(
arguments
)
}
@Test
def
testOutputTypeBcf
()
=
{
val
tmp
=
File
.
createTempFile
(
"VcfFilter"
,
".bcf"
)
tmp
.
deleteOnExit
()
val
tmp
_p
ath
=
tmp
.
getAbsolutePath
val
arguments
:
Array
[
String
]
=
Array
(
"-I"
,
vepped
_p
ath
,
"-o"
,
tmp
_p
ath
)
val
tmp
P
ath
=
tmp
.
getAbsolutePath
val
arguments
:
Array
[
String
]
=
Array
(
"-I"
,
vepped
P
ath
,
"-o"
,
tmp
P
ath
)
main
(
arguments
)
}
@Test
def
testOutputTypeVcfGz
()
=
{
val
tmp
=
File
.
createTempFile
(
"VcfFilter"
,
".vcf.gz"
)
tmp
.
deleteOnExit
()
val
tmp
_p
ath
=
tmp
.
getAbsolutePath
val
arguments
:
Array
[
String
]
=
Array
(
"-I"
,
vepped
_p
ath
,
"-o"
,
tmp
_p
ath
)
val
tmp
P
ath
=
tmp
.
getAbsolutePath
val
arguments
:
Array
[
String
]
=
Array
(
"-I"
,
vepped
P
ath
,
"-o"
,
tmp
P
ath
)
main
(
arguments
)
}
...
...
@@ -73,22 +73,22 @@ class VcfFilterTest extends TestNGSuite with MockitoSugar with Matchers {
*/
val
tmp
=
File
.
createTempFile
(
"VCfFilter"
,
".vcf.gz"
)
tmp
.
deleteOnExit
()
val
tmp
_p
ath
=
tmp
.
getAbsolutePath
val
arguments
:
Array
[
String
]
=
Array
(
"-I"
,
vepped
_p
ath
,
"-o"
,
tmp
_p
ath
,
val
tmp
P
ath
=
tmp
.
getAbsolutePath
val
arguments
:
Array
[
String
]
=
Array
(
"-I"
,
vepped
P
ath
,
"-o"
,
tmp
P
ath
,
"--mustHaveGenotype"
,
"Sample_101:HET"
)
main
(
arguments
)
val
size
=
new
VCFFileReader
(
new
File
(
tmp
_p
ath
),
false
).
size
val
size
=
new
VCFFileReader
(
new
File
(
tmp
P
ath
),
false
).
size
size
shouldBe
1
val
tmp2
=
File
.
createTempFile
(
"VcfFilter"
,
".vcf.gz"
)
tmp2
.
deleteOnExit
()
val
tmp
2_p
ath
=
tmp2
.
getAbsolutePath
val
arguments2
:
Array
[
String
]
=
Array
(
"-I"
,
vepped
_p
ath
,
"-o"
,
tmp
2_p
ath
,
val
tmp
P
ath
2
=
tmp2
.
getAbsolutePath
val
arguments2
:
Array
[
String
]
=
Array
(
"-I"
,
vepped
P
ath
,
"-o"
,
tmp
P
ath
2
,
"--mustHaveGenotype"
,
"Sample_101:HOM_VAR"
)
main
(
arguments2
)
val
size2
=
new
VCFFileReader
(
new
File
(
tmp
2_p
ath
),
false
).
size
val
size2
=
new
VCFFileReader
(
new
File
(
tmp
P
ath
2
),
false
).
size
size2
shouldBe
0
}
...
...
public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
View file @
00a24e74
...
...
@@ -31,7 +31,7 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
var
inputR1
:
File
=
_
@Input
(
doc
=
"R2 fastq file (gzipped allowed)"
,
shortName
=
"R2"
,
required
=
false
)
var
input
_
R2
:
Option
[
File
]
=
None
var
inputR2
:
Option
[
File
]
=
None
/** Skip Trim fastq files */
var
skipTrim
:
Boolean
=
config
(
"skip_trim"
,
default
=
false
)
...
...
@@ -48,13 +48,13 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
/** Returns files to store in summary */
def
summaryFiles
:
Map
[
String
,
File
]
=
{
Map
(
"input_R1"
->
inputR1
,
"output_R1"
->
fastqR1Qc
)
++
(
if
(
paired
)
Map
(
"input_R2"
->
input
_
R2
.
get
,
"output_R2"
->
fastqR2Qc
.
get
)
else
Map
())
(
if
(
paired
)
Map
(
"input_R2"
->
inputR2
.
get
,
"output_R2"
->
fastqR2Qc
.
get
)
else
Map
())
}
/** returns settings to store in summary */
def
summarySettings
=
Map
(
"skip_trim"
->
skipTrim
,
"skip_clip"
->
skipClip
,
"paired"
->
paired
)
var
paired
:
Boolean
=
input
_
R2
.
isDefined
var
paired
:
Boolean
=
inputR2
.
isDefined
var
R1Name
:
String
=
_
var
R2Name
:
String
=
_
...
...
@@ -80,13 +80,13 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
require
(
sampleId
!=
null
,
"Missing sample ID on flexiprep module"
)
require
(
libId
!=
null
,
"Missing library ID on flexiprep module"
)
paired
=
input
_
R2
.
isDefined
paired
=
inputR2
.
isDefined
inputFiles
:+=
new
InputFile
(
inputR1
)
input
_
R2
.
foreach
(
inputFiles
:+=
new
InputFile
(
_
))
inputR2
.
foreach
(
inputFiles
:+=
new
InputFile
(
_
))
R1Name
=
getUncompressedFileName
(
inputR1
)
input
_
R2
.
foreach
{
fileR2
=>
inputR2
.
foreach
{
fileR2
=>
paired
=
true
R2Name
=
getUncompressedFileName
(
fileR2
)
}
...
...
@@ -96,7 +96,7 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
def
biopetScript
()
{
runInitialJobs
()
if
(
paired
)
runTrimClip
(
inputR1
,
input
_
R2
,
outputDir
)
if
(
paired
)
runTrimClip
(
inputR1
,
inputR2
,
outputDir
)
else
runTrimClip
(
inputR1
,
outputDir
)
val
R1Files
=
for
((
k
,
v
)
<-
outputFiles
if
k
.
endsWith
(
"output_R1"
))
yield
v
...
...
@@ -107,7 +107,7 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
/** Add init non chunkable jobs */
def
runInitialJobs
()
{
outputFiles
+=
(
"fastq_input_R1"
->
inputR1
)
if
(
paired
)
outputFiles
+=
(
"fastq_input_R2"
->
input
_
R2
.
get
)
if
(
paired
)
outputFiles
+=
(
"fastq_input_R2"
->
inputR2
.
get
)
fastqcR1
=
Fastqc
(
this
,
inputR1
,
new
File
(
outputDir
,
R1Name
+
".fastqc/"
))
add
(
fastqcR1
)
...
...
@@ -116,7 +116,7 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
val
validateFastq
=
new
ValidateFastq
(
this
)
validateFastq
.
r1Fastq
=
inputR1
validateFastq
.
r2Fastq
=
input
_
R2
validateFastq
.
r2Fastq
=
inputR2
validateFastq
.
jobOutputFile
=
new
File
(
outputDir
,
".validate_fastq.log.out"
)
add
(
validateFastq
)
...
...
@@ -128,7 +128,7 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
}
if
(
paired
)
{
fastqcR2
=
Fastqc
(
this
,
input
_
R2
.
get
,
new
File
(
outputDir
,
R2Name
+
".fastqc/"
))
fastqcR2
=
Fastqc
(
this
,
inputR2
.
get
,
new
File
(
outputDir
,
R2Name
+
".fastqc/"
))
add
(
fastqcR2
)
addSummarizable
(
fastqcR2
,
"fastqc_R2"
)
outputFiles
+=
(
"fastqc_R2"
->
fastqcR2
.
output
)
...
...
@@ -140,7 +140,7 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
addSummarizable
(
seqstatR1
,
"seqstat_R1"
)
if
(
paired
)
{
val
seqstatR2
=
SeqStat
(
this
,
input
_
R2
.
get
,
outputDir
)
val
seqstatR2
=
SeqStat
(
this
,
inputR2
.
get
,
outputDir
)
seqstatR2
.
isIntermediate
=
true
add
(
seqstatR2
)
addSummarizable
(
seqstatR2
,
"seqstat_R2"
)
...
...
public/flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepTest.scala
View file @
00a24e74
...
...
@@ -71,7 +71,7 @@ class FlexiprepTest extends TestNGSuite with Matchers {
val
flexiprep
:
Flexiprep
=
initPipeline
(
map
)
flexiprep
.
inputR1
=
(
if
(
zipped
)
FlexiprepTest
.
r1Zipped
else
FlexiprepTest
.
r1
)
if
(
paired
)
flexiprep
.
input
_
R2
=
Some
((
if
(
zipped
)
FlexiprepTest
.
r2Zipped
else
FlexiprepTest
.
r2
))
if
(
paired
)
flexiprep
.
inputR2
=
Some
((
if
(
zipped
)
FlexiprepTest
.
r2Zipped
else
FlexiprepTest
.
r2
))
flexiprep
.
sampleId
=
Some
(
"1"
)
flexiprep
.
libId
=
Some
(
"1"
)
flexiprep
.
script
()
...
...
public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala
View file @
00a24e74
...
...
@@ -98,7 +98,7 @@ class Gears(val root: Configurable) extends QScript with MultiSampleQScript { qs
flexiprep
.
sampleId
=
Some
(
sampleId
)
flexiprep
.
libId
=
Some
(
libId
)
flexiprep
.
inputR1
=
config
(
"R1"
)
flexiprep
.
input
_
R2
=
config
(
"R2"
)
flexiprep
.
inputR2
=
config
(
"R2"
)
flexiprep
.
outputDir
=
new
File
(
libDir
,
"flexiprep"
)
lazy
val
gs
=
new
GearsSingle
(
qscript
)
...
...
@@ -109,7 +109,7 @@ class Gears(val root: Configurable) extends QScript with MultiSampleQScript { qs
/** Function that add library jobs */
protected
def
addJobs
()
:
Unit
=
{
inputFiles
:+=
InputFile
(
flexiprep
.
inputR1
,
config
(
"R1_md5"
))
flexiprep
.
input
_
R2
.
foreach
(
inputFiles
:+=
InputFile
(
_
,
config
(
"R2_md5"
)))
flexiprep
.
inputR2
.
foreach
(
inputFiles
:+=
InputFile
(
_
,
config
(
"R2_md5"
)))
add
(
flexiprep
)
gs
.
fastqR1
=
Some
(
flexiprep
.
fastqR1Qc
)
...
...
public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingle.scala
View file @
00a24e74
...
...
@@ -80,7 +80,7 @@ class GearsSingle(val root: Configurable) extends QScript with SummaryQScript wi
if
(!
skipFlexiprep
)
{
val
flexiprep
=
new
Flexiprep
(
this
)
flexiprep
.
inputR1
=
r1
flexiprep
.
input
_
R2
=
r2
flexiprep
.
inputR2
=
r2
flexiprep
.
outputDir
=
new
File
(
outputDir
,
"flexiprep"
)
add
(
flexiprep
)
(
flexiprep
.
fastqR1Qc
,
flexiprep
.
fastqR2Qc
)
...
...
public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
View file @
00a24e74
...
...
@@ -167,7 +167,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
if
(!
skipFlexiprep
)
{
flexiprep
.
outputDir
=
new
File
(
outputDir
,
"flexiprep"
)
flexiprep
.
inputR1
=
inputR1
flexiprep
.
input
_
R2
=
inputR2
flexiprep
.
inputR2
=
inputR2
flexiprep
.
sampleId
=
this
.
sampleId
flexiprep
.
libId
=
this
.
libId
flexiprep
.
init
()
...
...
@@ -184,7 +184,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
if
(
paired
)
Some
(
new
File
(
chunkDir
,
inputR2
.
get
.
getName
))
else
None
)
}).
toMap
else
if
(
skipFlexiprep
)
Map
(
outputDir
->
(
inputR1
,
if
(
paired
)
inputR2
else
None
))
else
Map
(
outputDir
->
(
flexiprep
.
inputR1
,
flexiprep
.
input
_
R2
))
else
Map
(
outputDir
->
(
flexiprep
.
inputR1
,
flexiprep
.
inputR2
))
}
if
(
chunking
)
{
...
...
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