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biopet.biopet
Commits
091a2657
Commit
091a2657
authored
Oct 03, 2016
by
Peter van 't Hof
Browse files
Fixed input files
parent
4245609f
Changes
2
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Inline
Side-by-side
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/centrifuge/Centrifuge.scala
View file @
091a2657
...
...
@@ -18,7 +18,6 @@ class Centrifuge(val root: Configurable) extends BiopetCommandLineFunction with
@Input
(
doc
=
"Input: FastQ or FastA"
,
required
=
false
)
var
inputR2
:
Option
[
File
]
=
None
@Input
(
doc
=
"Centrifuge index prefix"
,
required
=
true
)
var
index
:
File
=
config
(
"centrifuge_index"
)
@Output
(
doc
=
"Output with hits per sequence"
)
...
...
@@ -37,6 +36,13 @@ class Centrifuge(val root: Configurable) extends BiopetCommandLineFunction with
/** Regex to get version from version command output */
def
versionRegex
:
Regex
=
".* version (.*)"
.
r
override
def
beforeGraph
()
:
Unit
=
{
super
.
beforeGraph
()
deps
:+=
index
+
".1.cf"
deps
:+=
index
+
".2.cf"
deps
:+=
index
+
".3.cf"
}
/**
* This function needs to be implemented to define the command that is executed
*
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/centrifuge/CentrifugeKreport.scala
View file @
091a2657
...
...
@@ -16,7 +16,6 @@ class CentrifugeKreport(val root: Configurable) extends BiopetCommandLineFunctio
@Output
(
doc
=
"Output report"
)
var
output
:
File
=
_
@Input
(
doc
=
"Centrifuge index prefix"
,
required
=
true
)
var
index
:
File
=
config
(
"centrifuge_index"
,
namespace
=
"centrifuge"
)
var
onlyUnique
:
Boolean
=
config
(
"only_unique"
,
default
=
false
)
...
...
@@ -30,6 +29,13 @@ class CentrifugeKreport(val root: Configurable) extends BiopetCommandLineFunctio
executable
=
config
(
"exe"
,
default
=
"centrifuge-kreport"
,
freeVar
=
false
)
override
def
beforeGraph
()
:
Unit
=
{
super
.
beforeGraph
()
deps
:+=
index
+
".1.cf"
deps
:+=
index
+
".2.cf"
deps
:+=
index
+
".3.cf"
}
def
cmdLine
=
executable
+
conditional
(
onlyUnique
,
"--only-unique"
)
+
conditional
(
showZeros
,
"--show-zeros"
)
+
...
...
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