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biopet.biopet
Commits
8bed40ff
Commit
8bed40ff
authored
Mar 10, 2015
by
bow
Browse files
Fix missing wiggle jobs
parent
57622630
Changes
1
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Inline
Side-by-side
public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
View file @
8bed40ff
...
...
@@ -31,6 +31,7 @@ import nl.lumc.sasc.biopet.extensions.{ HtseqCount, Ln }
import
nl.lumc.sasc.biopet.extensions.picard.
{
CollectRnaSeqMetrics
,
SortSam
,
MergeSamFiles
}
import
nl.lumc.sasc.biopet.extensions.samtools.SamtoolsView
import
nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics
import
nl.lumc.sasc.biopet.pipelines.bamtobigwig.Bam2Wig
import
nl.lumc.sasc.biopet.pipelines.mapping.Mapping
import
nl.lumc.sasc.biopet.pipelines.gentrap.extensions.
{
CustomVarScan
,
Pdflatex
,
RawBaseCounter
}
import
nl.lumc.sasc.biopet.pipelines.gentrap.scripts.
{
AggrBaseCount
,
PdfReportTemplateWriter
,
PlotHeatmap
}
...
...
@@ -725,6 +726,10 @@ class Gentrap(val root: Configurable) extends QScript with MultiSampleQScript wi
addSummaryQScript
(
m
)
case
None
=>
;
}
// add bigwig output, also per-strand when possible
addAll
(
Bam2Wig
(
qscript
,
alnFile
).
functions
)
alnFilePlusStrand
.
collect
{
case
f
=>
addAll
(
Bam2Wig
(
qscript
,
f
).
functions
)
}
alnFileMinusStrand
.
collect
{
case
f
=>
addAll
(
Bam2Wig
(
qscript
,
f
).
functions
)
}
// add strand-specific jobs if defined
alnPlusStrandJobs
.
foreach
(
_
.
addAllJobs
())
alnMinusStrandJobs
.
foreach
(
_
.
addAllJobs
())
...
...
@@ -771,6 +776,9 @@ class Gentrap(val root: Configurable) extends QScript with MultiSampleQScript wi
def
collectRnaSeqMetricsJob
:
CollectRnaSeqMetrics
=
makeCollectRnaSeqMetricsJob
(
alnFile
,
createFile
(
".rna_metrics"
),
Option
(
createFile
(
".coverage_bias.pdf"
)))
/** Wiggle track job */
private
lazy
val
bam2wigModule
:
Bam2Wig
=
Bam2Wig
(
qscript
,
alnFile
)
/** Per-library mapping job */
def
mappingJob
:
Mapping
=
{
val
job
=
new
Mapping
(
qscript
)
...
...
@@ -787,6 +795,8 @@ class Gentrap(val root: Configurable) extends QScript with MultiSampleQScript wi
def
addJobs
()
:
Unit
=
{
// create per-library alignment file
addAll
(
mappingJob
.
functions
)
// add bigwig track
addAll
(
bam2wigModule
.
functions
)
// create RNA metrics job
add
(
collectRnaSeqMetricsJob
)
addSummarizable
(
collectRnaSeqMetricsJob
,
"rna_metrics"
)
...
...
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