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biopet.biopet
Commits
4b348b21
Commit
4b348b21
authored
Mar 09, 2015
by
bow
Browse files
Update gentrap summary and stats
parent
0c25f894
Changes
1
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Inline
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public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
View file @
4b348b21
...
...
@@ -244,9 +244,15 @@ class Gentrap(val root: Configurable) extends QScript with MultiSampleQScript wi
def
summaryFile
:
File
=
new
File
(
outputDir
,
"gentrap.summary.json"
)
/** Files that will be listed in the summary file */
def
summaryFiles
:
Map
[
String
,
File
]
=
def
summaryFiles
:
Map
[
String
,
File
]
=
Map
(
"annotation_refflat"
->
annotationRefFlat
)
++
Map
(
"annotation_gtf"
->
annotationGtf
,
"annotation_bed"
->
annotationBed
,
"ribosome_refflat"
->
ribosomalRefFlat
).
collect
{
case
(
key
,
Some
(
value
))
=>
key
->
value
}
++
mergeTableJobs
.
collect
{
case
(
key
,
Some
(
value
))
=>
key
->
value
.
output
}
++
heatmapJobs
.
collect
{
case
(
key
,
Some
(
value
))
=>
key
->
value
.
output
}
heatmapJobs
.
collect
{
case
(
key
,
Some
(
value
))
=>
key
->
value
.
output
}
/** Statistics shown in the summary file */
def
summaryStats
:
Map
[
String
,
Any
]
=
Map
()
...
...
@@ -254,14 +260,12 @@ class Gentrap(val root: Configurable) extends QScript with MultiSampleQScript wi
/** Pipeline settings shown in the summary file */
def
summarySettings
:
Map
[
String
,
Any
]
=
Map
(
"aligner"
->
aligner
,
"expression_measures"
->
expMeasures
.
map
(
_
.
toString
),
"strand_protocol"
->
strandProtocol
,
"annotation_refflat"
->
annotationRefFlat
,
"expression_measures"
->
expMeasures
.
toList
.
map
(
_
.
toString
),
"strand_protocol"
->
strandProtocol
.
toString
,
"call_variants"
->
callVariants
,
"remove_ribosomal_reads"
->
removeRibosomalReads
,
"version"
->
version
)
++
Map
(
"annotation_gtf"
->
annotationGtf
,
"annotation_bed"
->
annotationBed
).
collect
{
case
(
key
,
Some
(
value
))
=>
key
->
value
}
)
/** Job for writing PDF report template */
protected
lazy
val
pdfTemplateJob
:
PdfReportTemplateWriter
=
{
...
...
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