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biopet.biopet
Commits
45200c55
Commit
45200c55
authored
Feb 06, 2015
by
Peter van 't Hof
Browse files
Make input and output required
parent
97eb666f
Changes
1
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Inline
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public/bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala
View file @
45200c55
...
...
@@ -13,10 +13,10 @@ import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
class
Bam2Wig
(
val
root
:
Configurable
)
extends
QScript
with
BiopetQScript
{
def
this
()
=
this
(
null
)
@Input
@Input
(
doc
=
""
,
required
=
true
)
var
bamFile
:
File
=
_
@Output
@Output
(
doc
=
""
,
required
=
true
)
var
bigWigFile
:
File
=
_
def
init
()
:
Unit
=
{
...
...
@@ -33,6 +33,7 @@ class Bam2Wig(val root: Configurable) extends QScript with BiopetQScript {
igvCount
.
input
=
bamFile
igvCount
.
genomeChromSizes
=
bs
.
chromSizesFile
igvCount
.
wig
=
Some
(
swapExt
(
outputDir
,
bamFile
,
".bam"
,
".wig"
))
add
(
igvCount
)
val
wigToBigWig
=
new
WigToBigWig
(
this
)
wigToBigWig
.
inputWigFile
=
igvCount
.
wig
.
get
...
...
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