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biopet.biopet
Commits
11faecb0
Commit
11faecb0
authored
Aug 28, 2014
by
Peter van 't Hof
Browse files
Placeholder for library tag counts
parent
8d6d72c9
Changes
1
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Inline
Side-by-side
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala
View file @
11faecb0
...
...
@@ -108,8 +108,11 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
mapping
.
biopetScript
addAll
(
mapping
.
functions
)
if
(
config
(
"library_counts"
,
default
=
false
).
getBoolean
)
if
(
config
(
"library_counts"
,
default
=
false
).
getBoolean
)
{
this
.
addBedtoolsCounts
(
mapping
.
outputFiles
(
"finalBamFile"
),
sampleID
+
"-"
+
runID
,
runDir
)
// TODO: Tag counts
}
outputFiles
+=
(
"FinalBam"
->
mapping
.
outputFiles
(
"finalBamFile"
))
}
else
this
.
logger
.
error
(
"Sample: "
+
sampleID
+
": No R1 found for run: "
+
runConfig
)
...
...
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