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biopet.biopet
Commits
8dee06e5
Commit
8dee06e5
authored
10 years ago
by
wyleung
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Pipeline fixes
parent
64d1f13a
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biopet-framework/pom.xml
+1
-1
1 addition, 1 deletion
biopet-framework/pom.xml
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala
+4
-5
4 additions, 5 deletions
...n/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala
with
5 additions
and
6 deletions
biopet-framework/pom.xml
+
1
−
1
View file @
8dee06e5
...
...
@@ -111,7 +111,7 @@
<verbose>
false
</verbose>
<useNativeGit>
true
</useNativeGit>
<dotGitDirectory>
${project.basedir}/../.git
</dotGitDirectory>
<skipPoms>
tru
e
</skipPoms>
<skipPoms>
fals
e
</skipPoms>
<generateGitPropertiesFile>
true
</generateGitPropertiesFile>
<generateGitPropertiesFilename>
src/main/resources/git.properties
</generateGitPropertiesFilename>
<failOnNoGitDirectory>
false
</failOnNoGitDirectory>
...
...
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biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala
+
4
−
5
View file @
8dee06e5
...
...
@@ -8,7 +8,6 @@ import nl.lumc.sasc.biopet.core.config.Configurable
import
nl.lumc.sasc.biopet.core.MultiSampleQScript
import
nl.lumc.sasc.biopet.core.PipelineCommand
import
nl.lumc.sasc.biopet.extensions.picard.MergeSamFiles
import
nl.lumc.sasc.biopet.extensions.sambamba.
{
SambambaIndex
,
SambambaMerge
}
import
nl.lumc.sasc.biopet.extensions.svcallers.pindel.Pindel
import
nl.lumc.sasc.biopet.extensions.svcallers.
{
Breakdancer
,
Clever
}
...
...
@@ -84,18 +83,18 @@ class Yamsvp(val root: Configurable) extends QScript with MultiSampleQScript {
mergeSamFiles
.
input
=
libraryBamfiles
mergeSamFiles
.
output
=
alignmentDir
+
sampleID
+
".merged.bam"
add
(
mergeSamFiles
)
val
bamIndex
=
SambambaIndex
(
root
,
mergeSamFiles
.
output
)
add
(
bamIndex
)
mergeSamFiles
.
output
}
else
null
val
bamIndex
=
SambambaIndex
(
root
,
bamFile
)
add
(
bamIndex
)
/// bamfile will be used as input for the SV callers. First run Clever
// val cleverVCF : File = sampleDir + "/" + sampleID + ".clever.vcf"
val
cleverDir
=
svcallingDir
+
sampleID
+
".clever/"
val
clever
=
Clever
(
this
,
bamFile
,
this
.
reference
,
svcallingDir
,
cleverDir
)
clever
.
deps
=
List
(
bamIndex
.
output
)
sampleOutput
.
vcf
+=
(
"clever"
->
List
(
clever
.
outputvcf
))
add
(
clever
)
...
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