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biopet.biopet
Commits
99ef67e0
Commit
99ef67e0
authored
Mar 03, 2016
by
Peter van 't Hof
Browse files
Fixed summary
parent
6b75aecd
Changes
3
Hide whitespace changes
Inline
Side-by-side
public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/ExtractUnmappedReads.scala
View file @
99ef67e0
...
...
@@ -29,7 +29,8 @@ class ExtractUnmappedReads(val root: Configurable) extends QScript with BiopetQS
}
def
fastqUnmappedR1
=
new
File
(
outputDir
,
s
"$outputName.unmapped.R1.fq.gz"
)
def
fastqUnmappedR2
=
new
File
(
outputDir
,
s
"$outputName.unmapped.R2.fq.gz"
)
def
fastqUnmappedR2
=
if
(
paired
)
Some
(
new
File
(
outputDir
,
s
"$outputName.unmapped.R2.fq.gz"
))
else
None
def
fastqUnmappedSingletons
=
new
File
(
outputDir
,
s
"$outputName.unmapped.singletons.fq.gz"
)
def
biopetScript
()
:
Unit
=
{
...
...
@@ -48,7 +49,7 @@ class ExtractUnmappedReads(val root: Configurable) extends QScript with BiopetQS
samToFastq
.
input
=
samtoolsViewSelectUnmapped
.
output
samToFastq
.
fastqR1
=
fastqUnmappedR1
if
(
paired
)
{
samToFastq
.
fastqR2
=
fastqUnmappedR2
samToFastq
.
fastqR2
=
fastqUnmappedR2
.
get
samToFastq
.
fastqUnpaired
=
fastqUnmappedSingletons
}
samToFastq
.
isIntermediate
=
!
config
(
"keep_unmapped_fastq"
,
default
=
false
).
asBoolean
...
...
public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsKraken.scala
View file @
99ef67e0
...
...
@@ -97,7 +97,7 @@ class GearsKraken(val root: Configurable) extends QScript with SummaryQScript wi
/** Statistics shown in the summary file */
def
summaryFiles
:
Map
[
String
,
File
]
=
outputFiles
+
(
"input_R1"
->
fastqR1
)
++
(
fastqR2
match
{
case
Some
(
file
)
=>
Map
(
"input_R
1
"
->
file
)
case
Some
(
file
)
=>
Map
(
"input_R
2
"
->
file
)
case
_
=>
Map
()
})
}
...
...
public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingle.scala
View file @
99ef67e0
...
...
@@ -97,7 +97,7 @@ class GearsSingle(val root: Configurable) extends QScript with SummaryQScript wi
extract
.
bamFile
=
bam
extract
.
outputName
=
outputName
add
(
extract
)
executeFlexiprep
(
extract
.
fastqUnmappedR1
,
Some
(
extract
.
fastqUnmappedR2
)
)
executeFlexiprep
(
extract
.
fastqUnmappedR1
,
extract
.
fastqUnmappedR2
)
case
_
=>
throw
new
IllegalArgumentException
(
"Missing input files"
)
}
...
...
@@ -159,6 +159,7 @@ class GearsSingle(val root: Configurable) extends QScript with SummaryQScript wi
def
summaryFiles
:
Map
[
String
,
File
]
=
Map
.
empty
++
(
if
(
bamFile
.
isDefined
)
Map
(
"input_bam"
->
bamFile
.
get
)
else
Map
())
++
(
if
(
fastqR1
.
isDefined
)
Map
(
"input_R1"
->
fastqR1
.
get
)
else
Map
())
++
(
if
(
fastqR2
.
isDefined
)
Map
(
"input_R2"
->
fastqR2
.
get
)
else
Map
())
++
outputFiles
}
...
...
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