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biopet.biopet
Commits
b8c07bd9
Commit
b8c07bd9
authored
Oct 03, 2016
by
Peter van 't Hof
Browse files
Adding more testing
parent
81797e5a
Changes
2
Hide whitespace changes
Inline
Side-by-side
sage/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala
View file @
b8c07bd9
...
...
@@ -23,7 +23,7 @@ import nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep
import
nl.lumc.sasc.biopet.pipelines.mapping.Mapping
import
nl.lumc.sasc.biopet.extensions.tools.SquishBed
import
nl.lumc.sasc.biopet.extensions.tools.
{
BedtoolsCoverageToCounts
,
PrefixFastq
,
SageCountFastq
,
SageCreateLibrary
,
SageCreateTagCounts
}
import
nl.lumc.sasc.biopet.utils.
{
ConfigUtils
,
Logging
}
import
nl.lumc.sasc.biopet.utils.Logging
import
org.broadinstitute.gatk.queue.QScript
class
Sage
(
val
root
:
Configurable
)
extends
QScript
with
MultiSampleQScript
{
...
...
@@ -139,14 +139,14 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
def
biopetScript
()
{
val
squishBed
=
new
SquishBed
(
this
)
squishBed
.
input
=
countBed
.
get
squishBed
.
output
=
new
File
(
outputDir
,
countBed
.
get
.
getName
.
stripSuffix
(
".bed"
)
+
".squish.bed"
)
squishBed
.
input
=
countBed
.
get
OrElse
(
null
)
squishBed
.
output
=
new
File
(
outputDir
,
countBed
.
get
OrElse
(
new
File
(
"fake"
))
.
getName
.
stripSuffix
(
".bed"
)
+
".squish.bed"
)
add
(
squishBed
)
squishedCountBed
=
squishBed
.
output
if
(
tagsLibrary
.
isEmpty
)
{
val
cdl
=
new
SageCreateLibrary
(
this
)
cdl
.
input
=
transcriptome
.
get
cdl
.
input
=
transcriptome
.
get
OrElse
(
null
)
cdl
.
output
=
new
File
(
outputDir
,
"taglib/tag.lib"
)
cdl
.
noAntiTagsOutput
=
new
File
(
outputDir
,
"taglib/no_antisense_genes.txt"
)
cdl
.
noTagsOutput
=
new
File
(
outputDir
,
"taglib/no_sense_genes.txt"
)
...
...
sage/src/test/scala/nl/lumc/sasc/biopet/pipelines/sage/SageTest.scala
View file @
b8c07bd9
...
...
@@ -33,9 +33,11 @@ class SageTest extends TestNGSuite with Matchers {
}
def
sample1
=
Array
(
false
,
true
)
def
sample2
=
Array
(
false
,
true
)
def
transcriptome
=
true
def
countBed
=
true
def
tagsLibrary
=
false
def
libraryCounts
:
Option
[
Boolean
]
=
None
@Test
(
dataProvider
=
"sageOptions"
)
def
testSage
(
f
:
String
,
sample1
:
Boolean
,
sample2
:
Boolean
)
:
Unit
=
{
...
...
@@ -43,13 +45,16 @@ class SageTest extends TestNGSuite with Matchers {
var
m
:
Map
[
String
,
Any
]
=
SageTest
.
config
if
(
sample1
)
m
=
ConfigUtils
.
mergeMaps
(
SageTest
.
sample1
,
m
)
if
(
sample2
)
m
=
ConfigUtils
.
mergeMaps
(
SageTest
.
sample2
,
m
)
ConfigUtils
.
mergeMaps
(
Map
(
// Config values
),
m
)
ConfigUtils
.
mergeMaps
(
(
if
(
transcriptome
)
Map
[
String
,
Any
](
"transcriptome"
->
SageTest
.
inputTouch
(
"trans.fa"
))
else
Map
[
String
,
Any
]())
++
(
if
(
countBed
)
Map
[
String
,
Any
](
"count_bed"
->
SageTest
.
inputTouch
(
"count.bed"
))
else
Map
[
String
,
Any
]())
++
(
if
(
tagsLibrary
)
Map
[
String
,
Any
](
"tags_library"
->
SageTest
.
inputTouch
(
"tablib"
))
else
Map
[
String
,
Any
]())
++
libraryCounts
.
map
(
"library_counts"
->
_
),
m
)
}
if
(!
sample1
&&
!
sample2
)
{
if
(
(!
sample1
&&
!
sample2
)
||
!
countBed
||
(!
transcriptome
&&
!
tagsLibrary
))
{
// When no samples
intercept
[
IllegalStateException
]
{
initPipeline
(
map
).
script
()
...
...
@@ -81,6 +86,25 @@ class SageTest extends TestNGSuite with Matchers {
}
}
class
SageNoBedTest
extends
SageTest
{
override
def
sample1
=
Array
(
true
)
override
def
sample2
=
Array
(
false
)
override
def
countBed
=
false
}
class
SageNoLibTest
extends
SageTest
{
override
def
sample1
=
Array
(
true
)
override
def
sample2
=
Array
(
false
)
override
def
transcriptome
=
false
override
def
tagsLibrary
=
false
}
class
SageLibraryCountsTest
extends
SageTest
{
override
def
sample1
=
Array
(
true
)
override
def
sample2
=
Array
(
false
)
override
def
libraryCounts
=
Some
(
true
)
}
object
SageTest
{
val
outputDir
=
Files
.
createTempDir
()
outputDir
.
deleteOnExit
()
...
...
@@ -107,8 +131,6 @@ object SageTest {
val
config
:
Map
[
String
,
Any
]
=
Map
(
"reference_fasta"
->
(
outputDir
+
File
.
separator
+
"ref.fa"
),
"output_dir"
->
outputDir
.
getAbsolutePath
,
"transcriptome"
->
inputTouch
(
"trans.fa"
),
"count_bed"
->
inputTouch
(
"count.bed"
),
"fastqc"
->
Map
(
"exe"
->
"test"
),
"seqtk"
->
Map
(
"exe"
->
"test"
),
"md5sum"
->
Map
(
"exe"
->
"test"
),
...
...
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