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biopet.biopet
Commits
ee4de907
Commit
ee4de907
authored
Jul 25, 2017
by
pjvan_thof
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parent
26ff1d93
Changes
4
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4 changed files
with
65 additions
and
65 deletions
+65
-65
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/stringtie/Stringtie.scala
.../nl/lumc/sasc/biopet/extensions/stringtie/Stringtie.scala
+25
-24
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/stringtie/StringtieMerge.scala
...umc/sasc/biopet/extensions/stringtie/StringtieMerge.scala
+37
-36
gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
...scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
+2
-1
gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/Stringtie.scala
...mc/sasc/biopet/pipelines/gentrap/measures/Stringtie.scala
+1
-4
No files found.
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/stringtie/Stringtie.scala
View file @
ee4de907
...
...
@@ -54,7 +54,8 @@ class Stringtie(val parent: Configurable)
/** Regex to get version from version command output */
def
versionRegex
:
Regex
=
".*"
.
r
def
cmdLine
:
String
=
required
(
executable
)
+
def
cmdLine
:
String
=
required
(
executable
)
+
required
(
inputBam
)
+
conditional
(
v
,
"-v"
)
+
required
(
"-p"
,
threads
)
+
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/stringtie/StringtieMerge.scala
View file @
ee4de907
...
...
@@ -39,7 +39,8 @@ class StringtieMerge(val parent: Configurable)
/** Regex to get version from version command output */
def
versionRegex
:
Regex
=
".*"
.
r
def
cmdLine
:
String
=
required
(
executable
)
+
def
cmdLine
:
String
=
required
(
executable
)
+
required
(
"--merge"
)
conditional
(
v
,
"-v"
)
+
required
(
"-p"
,
threads
)
+
...
...
@@ -53,4 +54,4 @@ class StringtieMerge(val parent: Configurable)
(
if
(
outputAsStdout
)
""
else
required
(
"-o"
,
outputGtf
))
+
repeat
(
inputGtfs
)
}
}
gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
View file @
ee4de907
...
...
@@ -305,7 +305,8 @@ object Gentrap extends PipelineCommand {
/** Enumeration of available expression measures */
object
ExpMeasures
extends
Enumeration
{
val
FragmentsPerGene
,
BaseCounts
,
CufflinksStrict
,
CufflinksGuided
,
CufflinksBlind
,
Stringtie
=
Value
val
FragmentsPerGene
,
BaseCounts
,
CufflinksStrict
,
CufflinksGuided
,
CufflinksBlind
,
Stringtie
=
Value
}
/** Enumeration of available strandedness */
...
...
gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/Stringtie.scala
View file @
ee4de907
...
...
@@ -22,10 +22,7 @@ import org.broadinstitute.gatk.queue.QScript
/**
* Created by pjvan_thof on 1/12/16.
*/
class
Stringtie
(
val
parent
:
Configurable
)
extends
QScript
with
Measurement
with
AnnotationGtf
{
class
Stringtie
(
val
parent
:
Configurable
)
extends
QScript
with
Measurement
with
AnnotationGtf
{
def
mergeArgs
=
MergeArgs
(
idCols
=
List
(
1
),
valCol
=
2
,
fallback
=
"0"
)
/** Pipeline itself */
...
...
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