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biopet.biopet
Commits
d4cad0b9
Commit
d4cad0b9
authored
Jan 13, 2015
by
Peter van 't Hof
Browse files
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parent
d5906682
Changes
1
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public/sage/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala
View file @
d4cad0b9
...
...
@@ -22,14 +22,13 @@ import nl.lumc.sasc.biopet.extensions.bedtools.BedtoolsCoverage
import
nl.lumc.sasc.biopet.extensions.picard.MergeSamFiles
import
nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep
import
nl.lumc.sasc.biopet.pipelines.mapping.Mapping
import
nl.lumc.sasc.biopet.
script
s.PrefixFastq
import
nl.lumc.sasc.biopet.
tool
s.PrefixFastq
import
nl.lumc.sasc.biopet.tools.BedtoolsCoverageToCounts
import
nl.lumc.sasc.biopet.scripts.SquishBed
import
nl.lumc.sasc.biopet.tools.SageCountFastq
import
nl.lumc.sasc.biopet.tools.SageCreateLibrary
import
nl.lumc.sasc.biopet.tools.SageCreateTagCounts
import
org.broadinstitute.gatk.queue.QScript
import
org.broadinstitute.gatk.queue.function._
class
Sage
(
val
root
:
Configurable
)
extends
QScript
with
MultiSampleQScript
{
def
this
()
=
this
(
null
)
...
...
@@ -142,17 +141,17 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
addAll
(
flexiprep
.
functions
)
val
flexiprepOutput
=
for
((
key
,
file
)
<-
flexiprep
.
outputFiles
if
key
.
endsWith
(
"output_R1"
))
yield
file
val
prefixFastq
=
PrefixFastq
.
apply
(
this
,
flexiprepOutput
.
head
,
runDir
)
prefixFastq
.
prefix
=
config
(
"sage_tag"
,
default
=
"CATG"
)
val
prefixFastq
=
PrefixFastq
(
this
,
flexiprepOutput
.
head
,
runDir
)
prefixFastq
.
prefix
Seq
=
config
(
"sage_tag"
,
default
=
"CATG"
)
prefixFastq
.
deps
+:=
flexiprep
.
outputFiles
(
"fastq_input_R1"
)
add
(
prefixFastq
)
libraryOutput
.
prefixFastq
=
prefixFastq
.
output
libraryOutput
.
prefixFastq
=
prefixFastq
.
output
Fastq
val
mapping
=
new
Mapping
(
this
)
mapping
.
skipFlexiprep
=
true
mapping
.
skipMarkduplicates
=
true
mapping
.
aligner
=
config
(
"aligner"
,
default
=
"bowtie"
)
mapping
.
input_R1
=
prefixFastq
.
output
mapping
.
input_R1
=
prefixFastq
.
output
Fastq
mapping
.
RGLB
=
runConfig
(
"ID"
).
toString
mapping
.
RGSM
=
sampleConfig
(
"ID"
).
toString
if
(
runConfig
.
contains
(
"PL"
))
mapping
.
RGPL
=
runConfig
(
"PL"
).
toString
...
...
@@ -165,7 +164,7 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
if
(
config
(
"library_counts"
,
default
=
false
).
asBoolean
)
{
addBedtoolsCounts
(
mapping
.
outputFiles
(
"finalBamFile"
),
sampleID
+
"-"
+
runID
,
runDir
)
addTablibCounts
(
prefixFastq
.
output
,
sampleID
+
"-"
+
runID
,
runDir
)
addTablibCounts
(
prefixFastq
.
output
Fastq
,
sampleID
+
"-"
+
runID
,
runDir
)
}
libraryOutput
.
mappedBamFile
=
mapping
.
outputFiles
(
"finalBamFile"
)
...
...
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