Skip to content
GitLab
Projects
Groups
Snippets
/
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
Mirrors
biopet.biopet
Commits
d16c8ad1
Commit
d16c8ad1
authored
Mar 09, 2017
by
Peter van 't Hof
Browse files
Fixing null pointer
parent
6025ff20
Changes
2
Hide whitespace changes
Inline
Side-by-side
flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/QcCommand.scala
View file @
d16c8ad1
...
...
@@ -123,7 +123,11 @@ class QcCommand(val parent: Configurable, val fastqc: Fastqc, val read: String)
Some
(
cutadapt
)
}
else
None
case
(
None
,
_
)
=>
None
case
(
c
,
_
)
=>
c
case
(
Some
(
c
),
_
)
=>
c
.
fastqInput
=
seqtk
.
output
c
.
fastqOutput
=
new
File
(
output
.
getParentFile
,
input
.
getName
+
".cutadapt.fq"
)
c
.
statsOutput
=
new
File
(
flexiprep
.
outputDir
,
s
"${flexiprep.sampleId.getOrElse("
x
")}-${flexiprep.libId.getOrElse("
x
")}.$read.clip.stats"
)
Some
(
c
)
}
trim
.
foreach
{
t
=>
...
...
flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepTest.scala
View file @
d16c8ad1
...
...
@@ -62,8 +62,11 @@ class FlexiprepTest extends TestNGSuite with Matchers {
private
var
dirs
:
List
[
File
]
=
Nil
@Test
(
dataProvider
=
"flexiprepOptions"
)
def
testFlexiprep
(
f
:
String
,
paired
:
Boolean
,
skipTrim
:
Boolean
,
skipClip
:
Boolean
,
zipped
:
Boolean
,
abortOnCorruptFastq
:
Boolean
)
=
{
def
testFlexiprep
(
f
:
String
,
paired
:
Boolean
,
skipTrim
:
Boolean
,
skipClip
:
Boolean
,
zipped
:
Boolean
,
abortOnCorruptFastq
:
Boolean
)
=
{
val
outputDir
=
FlexiprepTest
.
outputDir
dirs
:+=
outputDir
val
map
=
ConfigUtils
.
mergeMaps
(
Map
(
"output_dir"
->
outputDir
,
...
...
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment