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biopet.biopet
Commits
02733716
Commit
02733716
authored
Aug 25, 2015
by
Peter van 't Hof
Browse files
Fixed testing
parent
d4e45996
Changes
2
Hide whitespace changes
Inline
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public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
View file @
02733716
...
...
@@ -45,8 +45,11 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
/** Returns files to store in summary */
def
summaryFiles
:
Map
[
String
,
File
]
=
{
Map
(
"input_R1"
->
input_R1
,
"output_R1"
->
outputFiles
(
"output_R1_gzip"
))
++
(
if
(
paired
)
Map
(
"input_R2"
->
input_R2
.
get
,
"output_R2"
->
outputFiles
(
"output_R2_gzip"
))
else
Map
())
if
(!
skipTrim
||
!
skipClip
)
Map
(
"input_R1"
->
input_R1
,
"output_R1"
->
outputFiles
(
"output_R1_gzip"
))
++
(
if
(
paired
)
Map
(
"input_R2"
->
input_R2
.
get
,
"output_R2"
->
outputFiles
(
"output_R2_gzip"
))
else
Map
())
else
Map
(
"input_R1"
->
input_R1
)
++
(
if
(
paired
)
Map
(
"input_R2"
->
input_R2
.
get
)
else
Map
())
}
/** returns settings to store in summary */
...
...
public/flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepTest.scala
View file @
02733716
...
...
@@ -84,7 +84,7 @@ class FlexiprepTest extends TestNGSuite with Matchers {
flexiprep
.
functions
.
count
(
_
.
isInstanceOf
[
Cutadapt
])
shouldBe
(
if
(
skipClip
)
0
else
if
(
paired
)
2
else
1
)
flexiprep
.
functions
.
count
(
_
.
isInstanceOf
[
FastqSync
])
shouldBe
(
if
(
skipClip
)
0
else
if
(
paired
)
1
else
0
)
flexiprep
.
functions
.
count
(
_
.
isInstanceOf
[
Sickle
])
shouldBe
(
if
(
skipTrim
)
0
else
1
)
flexiprep
.
functions
.
count
(
_
.
isInstanceOf
[
Gzip
])
shouldBe
(
if
(
paired
)
2
else
1
)
flexiprep
.
functions
.
count
(
_
.
isInstanceOf
[
Gzip
])
shouldBe
(
if
(
skipClip
&&
skipTrim
)
0
else
if
(
paired
)
2
else
1
)
}
// remove temporary run directory all tests in the class have been run
...
...
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