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biopet.biopet
Commits
6ac2ce38
Commit
6ac2ce38
authored
Oct 29, 2015
by
Peter van 't Hof
Browse files
Added reference to bamMetrics
parent
25d38d41
Changes
1
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Inline
Side-by-side
public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
View file @
6ac2ce38
...
...
@@ -19,7 +19,7 @@ import java.io.File
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
nl.lumc.sasc.biopet.core.summary.SummaryQScript
import
nl.lumc.sasc.biopet.core.
{
BiopetFifoPipe
,
PipelineCommand
,
SampleLibraryTag
}
import
nl.lumc.sasc.biopet.core.
{
Reference
,
BiopetFifoPipe
,
PipelineCommand
,
SampleLibraryTag
}
import
nl.lumc.sasc.biopet.extensions.bedtools.
{
BedtoolsCoverage
,
BedtoolsIntersect
}
import
nl.lumc.sasc.biopet.extensions.picard._
import
nl.lumc.sasc.biopet.extensions.samtools.SamtoolsFlagstat
...
...
@@ -27,7 +27,11 @@ import nl.lumc.sasc.biopet.pipelines.bammetrics.scripts.CoverageStats
import
nl.lumc.sasc.biopet.extensions.tools.BiopetFlagstat
import
org.broadinstitute.gatk.queue.QScript
class
BamMetrics
(
val
root
:
Configurable
)
extends
QScript
with
SummaryQScript
with
SampleLibraryTag
{
class
BamMetrics
(
val
root
:
Configurable
)
extends
QScript
with
SummaryQScript
with
SampleLibraryTag
with
Reference
{
def
this
()
=
this
(
null
)
@Input
(
doc
=
"Bam File"
,
shortName
=
"BAM"
,
required
=
true
)
...
...
@@ -51,7 +55,8 @@ class BamMetrics(val root: Configurable) extends QScript with SummaryQScript wit
}
/** returns files to store in summary */
def
summaryFiles
=
Map
(
"input_bam"
->
inputBam
)
++
def
summaryFiles
=
Map
(
"reference"
->
referenceFasta
(),
"input_bam"
->
inputBam
)
++
ampliconBedFile
.
map
(
"amplicon"
->
_
).
toMap
++
ampliconBedFile
.
map
(
x
=>
"roi_"
+
x
.
getName
.
stripSuffix
(
".bed"
)
->
x
).
toMap
...
...
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