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biopet.biopet
Commits
565f3979
Commit
565f3979
authored
Jan 08, 2016
by
Peter van 't Hof
Browse files
Fixed rna metrics
parent
d9c88772
Changes
4
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Inline
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public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
View file @
565f3979
...
...
@@ -39,7 +39,6 @@ class BamMetrics(val root: Configurable) extends QScript
var
inputBam
:
File
=
_
/** Settings for CollectRnaSeqMetrics */
var
rnaMetricsSettings
:
Map
[
String
,
String
]
=
Map
()
var
transcriptRefFlatFile
:
Option
[
File
]
=
config
(
"transcript_refflat"
)
/** return location of summary file */
...
...
@@ -107,8 +106,6 @@ class BamMetrics(val root: Configurable) extends QScript
rnaMetrics
.
output
=
swapExt
(
outputDir
,
inputBam
,
".bam"
,
".rna.metrics"
)
rnaMetrics
.
chartOutput
=
Some
(
swapExt
(
outputDir
,
inputBam
,
".bam"
,
".rna.metrics.pdf"
))
rnaMetrics
.
refFlat
=
transcriptRefFlatFile
.
get
rnaMetrics
.
ribosomalIntervals
=
rnaMetricsSettings
.
get
(
"ribosomal_intervals"
).
collect
{
case
n
=>
new
File
(
n
)
}
rnaMetrics
.
strandSpecificity
=
rnaMetricsSettings
.
get
(
"strand_specificity"
)
add
(
rnaMetrics
)
addSummarizable
(
rnaMetrics
,
"rna"
)
}
...
...
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bowtie/Bowtie2.scala
View file @
565f3979
...
...
@@ -2,10 +2,10 @@ package nl.lumc.sasc.biopet.extensions.bowtie
import
java.io.File
import
nl.lumc.sasc.biopet.core.
{
BiopetCommandLineFunction
,
Reference
,
Version
}
import
nl.lumc.sasc.biopet.core.
{
BiopetCommandLineFunction
,
Reference
,
Version
}
import
nl.lumc.sasc.biopet.utils.Logging
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
/**
* Extension for bowtie 2
...
...
public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
View file @
565f3979
...
...
@@ -19,13 +19,13 @@ import java.io.File
import
nl.lumc.sasc.biopet.FullVersion
import
nl.lumc.sasc.biopet.core._
import
nl.lumc.sasc.biopet.extensions.picard.
{
MergeSamFiles
,
SortSam
}
import
nl.lumc.sasc.biopet.extensions.picard.
{
MergeSamFiles
,
SortSam
}
import
nl.lumc.sasc.biopet.extensions.samtools.SamtoolsView
import
nl.lumc.sasc.biopet.extensions.tools.
{
MergeTables
,
WipeReads
}
import
nl.lumc.sasc.biopet.extensions.
{
HtseqCount
,
Ln
}
import
nl.lumc.sasc.biopet.extensions.tools.
{
MergeTables
,
WipeReads
}
import
nl.lumc.sasc.biopet.extensions.
{
HtseqCount
,
Ln
}
import
nl.lumc.sasc.biopet.pipelines.bamtobigwig.Bam2Wig
import
nl.lumc.sasc.biopet.pipelines.gentrap.extensions.
{
CustomVarScan
,
Pdflatex
,
RawBaseCounter
}
import
nl.lumc.sasc.biopet.pipelines.gentrap.scripts.
{
AggrBaseCount
,
PdfReportTemplateWriter
,
PlotHeatmap
}
import
nl.lumc.sasc.biopet.pipelines.gentrap.extensions.
{
CustomVarScan
,
Pdflatex
,
RawBaseCounter
}
import
nl.lumc.sasc.biopet.pipelines.gentrap.scripts.
{
AggrBaseCount
,
PdfReportTemplateWriter
,
PlotHeatmap
}
import
nl.lumc.sasc.biopet.pipelines.mapping.MultisampleMappingTrait
import
nl.lumc.sasc.biopet.utils.Logging
import
nl.lumc.sasc.biopet.utils.config._
...
...
@@ -98,17 +98,6 @@ class Gentrap(val root: Configurable) extends QScript
/** Whether to do simple variant calling on RNA or not */
var
callVariants
:
Boolean
=
config
(
"call_variants"
,
default
=
false
)
/** Settings for all Picard CollectRnaSeqMetrics runs */
private
def
collectRnaSeqMetricsSettings
:
Map
[
String
,
String
]
=
Map
(
"strand_specificity"
->
(
strandProtocol
match
{
case
NonSpecific
=>
StrandSpecificity
.
NONE
.
toString
case
Dutp
=>
StrandSpecificity
.
SECOND_READ_TRANSCRIPTION_STRAND
.
toString
case
otherwise
=>
throw
new
IllegalStateException
(
otherwise
.
toString
)
}))
++
(
ribosomalRefFlat
match
{
case
Some
(
rbs
)
=>
Map
(
"ribosomal_intervals"
->
rbs
.
toString
)
case
None
=>
Map
()
})
/** Default pipeline config */
override
def
defaults
=
Map
(
"merge_strategy"
->
"preprocessmergesam"
,
...
...
@@ -117,6 +106,17 @@ class Gentrap(val root: Configurable) extends QScript
"batch"
->
4
,
"format"
->
"sam"
),
"bammetrics"
->
Map
(
"transcript_refflat"
->
annotationRefFlat
,
"collectrnaseqmetrics"
->
((
if
(
strandProtocol
!=
null
)
Map
(
"strand_specificity"
->
(
strandProtocol
match
{
case
NonSpecific
=>
StrandSpecificity
.
NONE
.
toString
case
Dutp
=>
StrandSpecificity
.
SECOND_READ_TRANSCRIPTION_STRAND
.
toString
case
otherwise
=>
throw
new
IllegalStateException
(
otherwise
.
toString
)
})
)
else
Map
())
++
(
if
(
ribosomalRefFlat
!=
null
)
ribosomalRefFlat
.
map
(
"ribosomal_intervals"
->
_
.
getAbsolutePath
).
toList
else
Nil
))
),
"cutadapt"
->
Map
(
"minimum_length"
->
20
),
// avoid conflicts when merging since the MarkDuplicate tags often cause merges to fail
"picard"
->
Map
(
...
...
public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
View file @
565f3979
...
...
@@ -20,7 +20,7 @@ import java.util.Date
import
nl.lumc.sasc.biopet.core._
import
nl.lumc.sasc.biopet.core.summary.SummaryQScript
import
nl.lumc.sasc.biopet.extensions.bowtie.
{
Bowtie2
,
Bowtie
}
import
nl.lumc.sasc.biopet.extensions.bowtie.
{
Bowtie2
,
Bowtie
}
import
nl.lumc.sasc.biopet.extensions.bwa.
{
BwaAln
,
BwaMem
,
BwaSampe
,
BwaSamse
}
import
nl.lumc.sasc.biopet.extensions.gmap.Gsnap
import
nl.lumc.sasc.biopet.extensions.picard.
{
AddOrReplaceReadGroups
,
MarkDuplicates
,
MergeSamFiles
,
ReorderSam
,
SortSam
}
...
...
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