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
cb6f9998
Commit
cb6f9998
authored
Feb 19, 2015
by
Sander Bollen
Browse files
fixing missing cutadapt mock values
parent
a7b54487
Changes
3
Hide whitespace changes
Inline
Side-by-side
public/carp/src/test/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpTest.scala
View file @
cb6f9998
...
...
@@ -39,7 +39,7 @@ class CarpTest extends TestNGSuite with Matchers {
def
testCarp
(
f
:
String
,
sample1
:
Boolean
,
sample2
:
Boolean
,
sample3
:
Boolean
,
threatment
:
Boolean
,
control
:
Boolean
)
:
Unit
=
{
val
map
=
{
var
m
=
ConfigUtils
.
mergeMaps
(
Map
(
"output_dir"
->
CarpTest
.
outputDir
),
CarpTest
.
excutables
)
),
CarpTest
.
ex
e
cutables
)
if
(
sample1
)
m
=
ConfigUtils
.
mergeMaps
(
CarpTest
.
sample1
,
m
.
toMap
)
if
(
sample2
)
m
=
ConfigUtils
.
mergeMaps
(
CarpTest
.
sample2
,
m
.
toMap
)
...
...
@@ -82,12 +82,13 @@ class CarpTest extends TestNGSuite with Matchers {
object
CarpTest
{
val
outputDir
=
Files
.
createTempDir
()
val
excutables
=
Map
(
val
ex
e
cutables
=
Map
(
"reference"
->
"test"
,
"seqstat"
->
Map
(
"exe"
->
"test"
),
"fastqc"
->
Map
(
"exe"
->
"test"
),
"seqtk"
->
Map
(
"exe"
->
"test"
),
"sickle"
->
Map
(
"exe"
->
"test"
),
"cutadapt"
->
Map
(
"exe"
->
"test"
),
"bwa"
->
Map
(
"exe"
->
"test"
),
"samtools"
->
Map
(
"exe"
->
"test"
),
"macs2"
->
Map
(
"exe"
->
"test"
),
...
...
public/flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepTest.scala
View file @
cb6f9998
...
...
@@ -48,7 +48,7 @@ class FlexiprepTest extends TestNGSuite with Matchers {
val
map
=
ConfigUtils
.
mergeMaps
(
Map
(
"output_dir"
->
FlexiprepTest
.
outputDir
,
"skip_trim"
->
skipTrim
,
"skip_clip"
->
skipClip
),
Map
(
FlexiprepTest
.
excutables
.
toSeq
:
_
*
))
),
Map
(
FlexiprepTest
.
ex
e
cutables
.
toSeq
:
_
*
))
val
flexiprep
:
Flexiprep
=
initPipeline
(
map
)
flexiprep
.
input_R1
=
new
File
(
flexiprep
.
outputDir
,
"bla_R1.fq"
+
(
if
(
zipped
)
".gz"
else
""
))
...
...
@@ -79,10 +79,11 @@ class FlexiprepTest extends TestNGSuite with Matchers {
object
FlexiprepTest
{
val
outputDir
=
Files
.
createTempDir
()
val
excutables
=
Map
(
val
ex
e
cutables
=
Map
(
"seqstat"
->
Map
(
"exe"
->
"test"
),
"fastqc"
->
Map
(
"exe"
->
"test"
),
"seqtk"
->
Map
(
"exe"
->
"test"
),
"sickle"
->
Map
(
"exe"
->
"test"
)
"sickle"
->
Map
(
"exe"
->
"test"
),
"cutadapt"
->
Map
(
"exe"
->
"test"
)
)
}
\ No newline at end of file
public/mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala
View file @
cb6f9998
...
...
@@ -57,7 +57,7 @@ class MappingTest extends TestNGSuite with Matchers {
"number_chunks"
->
chunks
,
"skip_markduplicates"
->
skipMarkDuplicate
,
"skip_flexiprep"
->
skipFlexiprep
),
Map
(
MappingTest
.
excutables
.
toSeq
:
_
*
))
),
Map
(
MappingTest
.
ex
e
cutables
.
toSeq
:
_
*
))
val
mapping
:
Mapping
=
initPipeline
(
map
)
mapping
.
input_R1
=
new
File
(
mapping
.
outputDir
,
"bla_R1.fq"
)
...
...
@@ -107,12 +107,13 @@ class MappingTest extends TestNGSuite with Matchers {
object
MappingTest
{
val
outputDir
=
Files
.
createTempDir
()
val
excutables
=
Map
(
val
ex
e
cutables
=
Map
(
"reference"
->
"test"
,
"seqstat"
->
Map
(
"exe"
->
"test"
),
"fastqc"
->
Map
(
"exe"
->
"test"
),
"seqtk"
->
Map
(
"exe"
->
"test"
),
"sickle"
->
Map
(
"exe"
->
"test"
),
"cutadapt"
->
Map
(
"exe"
->
"test"
),
"bwa"
->
Map
(
"exe"
->
"test"
),
"star"
->
Map
(
"exe"
->
"test"
),
"bowtie"
->
Map
(
"exe"
->
"test"
),
...
...
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