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biopet.biopet
Commits
20cd7b6d
Commit
20cd7b6d
authored
Oct 30, 2015
by
Peter van 't Hof
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Added input file checking
parent
b7743a6e
Changes
2
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2 changed files
with
9 additions
and
1 deletion
+9
-1
public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
...c/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
+1
-1
public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala
...ain/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala
+8
-0
No files found.
public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
View file @
20cd7b6d
...
...
@@ -119,5 +119,5 @@ trait BiopetQScript extends Configurable with GatkLogging {
}
object
BiopetQScript
{
protected
case
class
InputFile
(
file
:
File
,
md5
:
Option
[
String
]
=
None
)
case
class
InputFile
(
file
:
File
,
md5
:
Option
[
String
]
=
None
)
}
public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala
View file @
20cd7b6d
...
...
@@ -16,6 +16,7 @@
package
nl.lumc.sasc.biopet.pipelines.gears
import
nl.lumc.sasc.biopet.core.summary.SummaryQScript
import
nl.lumc.sasc.biopet.core.BiopetQScript.InputFile
import
nl.lumc.sasc.biopet.core.
{
PipelineCommand
,
SampleLibraryTag
}
import
nl.lumc.sasc.biopet.extensions.kraken.
{
Kraken
,
KrakenReport
}
import
nl.lumc.sasc.biopet.extensions.picard.SamToFastq
...
...
@@ -55,6 +56,13 @@ class Gears(val root: Configurable) extends QScript with SummaryQScript with Sam
.
getOrElse
(
"noName"
)
else
outputName
=
bamFile
.
map
(
_
.
getName
.
stripSuffix
(
".bam"
)).
getOrElse
(
"noName"
)
}
if
(
fastqR1
.
isDefined
)
{
fastqR1
.
foreach
(
inputFiles
:+=
InputFile
(
_
))
fastqR2
.
foreach
(
inputFiles
:+=
InputFile
(
_
))
}
else
{
inputFiles
:+=
InputFile
(
bamFile
.
get
)
}
}
override
def
reportClass
=
{
...
...
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