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biopet.biopet
Commits
f4fb8907
Commit
f4fb8907
authored
Oct 15, 2015
by
Peter van 't Hof
Browse files
Remove "reference" from testing
(cherry picked from commit
8bf162ad
)
parent
23a9cd94
Changes
8
Hide whitespace changes
Inline
Side-by-side
protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaTest.scala
View file @
f4fb8907
...
...
@@ -109,7 +109,6 @@ object ShivaTest {
"dir"
->
"test"
,
"vep_script"
->
"test"
,
"output_dir"
->
outputDir
,
"reference"
->
(
outputDir
+
File
.
separator
+
"ref.fa"
),
"reference_fasta"
->
(
outputDir
+
File
.
separator
+
"ref.fa"
),
"gatk_jar"
->
"test"
,
"samtools"
->
Map
(
"exe"
->
"test"
),
...
...
protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaVariantcallingTest.scala
View file @
f4fb8907
...
...
@@ -131,7 +131,6 @@ object ShivaVariantcallingTest {
"cache"
->
true
,
"dir"
->
"test"
,
"vep_script"
->
"test"
,
"reference"
->
(
outputDir
+
File
.
separator
+
"ref.fa"
),
"reference_fasta"
->
(
outputDir
+
File
.
separator
+
"ref.fa"
),
"gatk_jar"
->
"test"
,
"samtools"
->
Map
(
"exe"
->
"test"
),
...
...
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetrics.scala
View file @
f4fb8907
...
...
@@ -17,12 +17,13 @@ package nl.lumc.sasc.biopet.extensions.picard
import
java.io.File
import
nl.lumc.sasc.biopet.core.Reference
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
nl.lumc.sasc.biopet.core.summary.Summarizable
import
org.broadinstitute.gatk.utils.commandline.
{
Argument
,
Input
,
Output
}
/** Extension for picard CollectAlignmentSummaryMetrics */
class
CollectAlignmentSummaryMetrics
(
val
root
:
Configurable
)
extends
Picard
with
Summarizable
{
class
CollectAlignmentSummaryMetrics
(
val
root
:
Configurable
)
extends
Picard
with
Summarizable
with
Reference
{
javaMainClass
=
new
picard
.
analysis
.
CollectAlignmentSummaryMetrics
().
getClass
.
getName
@Input
(
doc
=
"The input SAM or BAM files to analyze. Must be coordinate sorted."
,
required
=
true
)
...
...
@@ -41,7 +42,7 @@ class CollectAlignmentSummaryMetrics(val root: Configurable) extends Picard with
var
output
:
File
=
_
@Argument
(
doc
=
"Reference file"
,
required
=
false
)
var
reference
:
File
=
config
(
"reference"
)
var
reference
:
File
=
_
@Argument
(
doc
=
"ASSUME_SORTED"
,
required
=
false
)
var
assumeSorted
:
Boolean
=
config
(
"assumeSorted"
,
default
=
true
)
...
...
@@ -52,6 +53,11 @@ class CollectAlignmentSummaryMetrics(val root: Configurable) extends Picard with
@Argument
(
doc
=
"STOP_AFTER"
,
required
=
false
)
var
stopAfter
:
Option
[
Long
]
=
config
(
"stopAfter"
)
override
def
beforeGraph
()
:
Unit
=
{
super
.
beforeGraph
()
if
(
reference
==
null
)
reference
=
referenceFasta
()
}
/** Returns command to execute */
override
def
cmdLine
=
super
.
cmdLine
+
required
(
"INPUT="
,
input
,
spaceSeparated
=
false
)
+
...
...
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetrics.scala
View file @
f4fb8907
...
...
@@ -17,6 +17,7 @@ package nl.lumc.sasc.biopet.extensions.picard
import
java.io.File
import
nl.lumc.sasc.biopet.core.Reference
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
nl.lumc.sasc.biopet.core.summary.Summarizable
import
org.broadinstitute.gatk.utils.commandline.
{
Argument
,
Input
,
Output
}
...
...
@@ -24,7 +25,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
import
scala.collection.immutable.Nil
/** Extension for picard CollectInsertSizeMetrics */
class
CollectInsertSizeMetrics
(
val
root
:
Configurable
)
extends
Picard
with
Summarizable
{
class
CollectInsertSizeMetrics
(
val
root
:
Configurable
)
extends
Picard
with
Summarizable
with
Reference
{
javaMainClass
=
new
picard
.
analysis
.
CollectInsertSizeMetrics
().
getClass
.
getName
@Input
(
doc
=
"The input SAM or BAM files to analyze. Must be coordinate sorted."
,
required
=
true
)
...
...
@@ -37,7 +38,7 @@ class CollectInsertSizeMetrics(val root: Configurable) extends Picard with Summa
protected
var
outputHistogram
:
File
=
null
@Argument
(
doc
=
"Reference file"
,
required
=
false
)
var
reference
:
File
=
config
(
"reference"
)
var
reference
:
File
=
_
@Argument
(
doc
=
"DEVIATIONS"
,
required
=
false
)
var
deviations
:
Option
[
Double
]
=
config
(
"deviations"
)
...
...
@@ -59,6 +60,7 @@ class CollectInsertSizeMetrics(val root: Configurable) extends Picard with Summa
override
def
beforeGraph
()
{
outputHistogram
=
new
File
(
output
+
".pdf"
)
if
(
reference
==
null
)
reference
=
referenceFasta
()
}
/** Returns command to execute */
...
...
public/carp/src/test/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpTest.scala
View file @
f4fb8907
...
...
@@ -116,7 +116,6 @@ object CarpTest {
copyFile
(
"ref.fa.fai"
)
val
executables
=
Map
(
"reference"
->
(
outputDir
+
File
.
separator
+
"ref.fa"
),
"reference_fasta"
->
(
outputDir
+
File
.
separator
+
"ref.fa"
),
"fastqc"
->
Map
(
"exe"
->
"test"
),
"seqtk"
->
Map
(
"exe"
->
"test"
),
...
...
public/gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala
View file @
f4fb8907
...
...
@@ -198,7 +198,6 @@ object GentrapTest {
copyFile
(
"ref.fa.fai"
)
val
executables
=
Map
(
"reference"
->
(
outputDir
+
File
.
separator
+
"ref.fa"
),
"reference_fasta"
->
(
outputDir
+
File
.
separator
+
"ref.fa"
),
"refFlat"
->
"test"
,
"annotation_gtf"
->
"test"
,
...
...
public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala
View file @
f4fb8907
...
...
@@ -109,7 +109,6 @@ object ShivaTest {
"cache"
->
true
,
"dir"
->
"test"
,
"vep_script"
->
"test"
,
"reference"
->
(
outputDir
+
File
.
separator
+
"ref.fa"
),
"reference_fasta"
->
(
outputDir
+
File
.
separator
+
"ref.fa"
),
"gatk_jar"
->
"test"
,
"samtools"
->
Map
(
"exe"
->
"test"
),
...
...
public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala
View file @
f4fb8907
...
...
@@ -112,7 +112,6 @@ object ShivaVariantcallingTest {
"cache"
->
true
,
"dir"
->
"test"
,
"vep_script"
->
"test"
,
"reference"
->
(
outputDir
+
File
.
separator
+
"ref.fa"
),
"reference_fasta"
->
(
outputDir
+
File
.
separator
+
"ref.fa"
),
"gatk_jar"
->
"test"
,
"samtools"
->
Map
(
"exe"
->
"test"
),
...
...
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