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biopet.biopet
Commits
48b7822f
Commit
48b7822f
authored
Mar 16, 2016
by
Peter van 't Hof
Browse files
Added wigle and tdf files to summary
parent
18184194
Changes
2
Hide whitespace changes
Inline
Side-by-side
public/bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala
View file @
48b7822f
...
...
@@ -38,6 +38,10 @@ class Bam2Wig(val root: Configurable) extends QScript with BiopetQScript {
inputFiles
:+=
new
InputFile
(
bamFile
)
}
def
outputWigleFile
=
new
File
(
outputDir
,
bamFile
.
getName
+
".wig"
)
def
outputTdfFile
=
new
File
(
outputDir
,
bamFile
.
getName
+
".tdf"
)
def
outputBwFile
=
new
File
(
outputDir
,
bamFile
.
getName
+
".bw"
)
def
biopetScript
()
:
Unit
=
{
val
bs
=
new
BamToChromSizes
(
this
)
bs
.
bamFile
=
bamFile
...
...
@@ -48,14 +52,14 @@ class Bam2Wig(val root: Configurable) extends QScript with BiopetQScript {
val
igvCount
=
new
IGVToolsCount
(
this
)
igvCount
.
input
=
bamFile
igvCount
.
genomeChromSizes
=
bs
.
chromSizesFile
igvCount
.
wig
=
Some
(
new
File
(
outputDir
,
bamFile
.
getName
+
".wig"
)
)
igvCount
.
tdf
=
Some
(
new
File
(
outputDir
,
bamFile
.
getName
+
".tdf"
)
)
igvCount
.
wig
=
Some
(
outputWigleFile
)
igvCount
.
tdf
=
Some
(
outputTdfFile
)
add
(
igvCount
)
val
wigToBigWig
=
new
WigToBigWig
(
this
)
wigToBigWig
.
inputWigFile
=
igvCount
.
wig
.
get
wigToBigWig
.
inputChromSizesFile
=
bs
.
chromSizesFile
wigToBigWig
.
outputBigWig
=
new
File
(
outputDir
,
bamFile
.
getName
+
".bw"
)
wigToBigWig
.
outputBigWig
=
outputBwFile
add
(
wigToBigWig
)
}
}
...
...
public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
View file @
48b7822f
...
...
@@ -109,7 +109,14 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
/** File to add to the summary */
def
summaryFiles
:
Map
[
String
,
File
]
=
Map
(
"output_bam"
->
finalBamFile
,
"input_R1"
->
inputR1
,
"reference"
->
referenceFasta
())
++
(
if
(
inputR2
.
isDefined
)
Map
(
"input_R2"
->
inputR2
.
get
)
else
Map
())
(
if
(
inputR2
.
isDefined
)
Map
(
"input_R2"
->
inputR2
.
get
)
else
Map
())
++
(
bam2wig
match
{
case
Some
(
b
)
=>
Map
(
"output_wigle"
->
b
.
outputWigleFile
,
"output_tdf"
->
b
.
outputTdfFile
,
"output_bigwig"
->
b
.
outputBwFile
)
case
_
=>
Map
()
})
/** Settings to add to summary */
def
summarySettings
=
Map
(
...
...
@@ -270,12 +277,15 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
add
(
gears
)
}
if
(
config
(
"generate_wig"
,
default
=
false
).
asBoolean
)
addAll
(
Bam2Wig
(
this
,
finalBamFile
).
functions
)
bam2wig
.
foreach
(
add
(
_
))
addSummaryJobs
()
}
protected
lazy
val
bam2wig
=
if
(
config
(
"generate_wig"
,
default
=
false
))
{
Some
(
Bam2Wig
(
this
,
finalBamFile
))
}
else
None
/** Add bwa aln jobs */
def
addBwaAln
(
R1
:
File
,
R2
:
Option
[
File
],
output
:
File
)
:
File
=
{
val
bwaAlnR1
=
new
BwaAln
(
this
)
...
...
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