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biopet.biopet
Commits
f5409cd1
Commit
f5409cd1
authored
Nov 05, 2015
by
Sander Bollen
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fix non-required arguments for manwe
parent
a06766d9
Changes
8
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8 changed files
with
17 additions
and
9 deletions
+17
-9
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweAnnotateBed.scala
.../lumc/sasc/biopet/extensions/manwe/ManweAnnotateBed.scala
+1
-1
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweAnnotateVcf.scala
.../lumc/sasc/biopet/extensions/manwe/ManweAnnotateVcf.scala
+1
-1
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweDataSourcesAnnotate.scala
...sc/biopet/extensions/manwe/ManweDataSourcesAnnotate.scala
+1
-1
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesAdd.scala
...l/lumc/sasc/biopet/extensions/manwe/ManweSamplesAdd.scala
+1
-1
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesAnnotateVariations.scala
...pet/extensions/manwe/ManweSamplesAnnotateVariations.scala
+1
-1
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesList.scala
.../lumc/sasc/biopet/extensions/manwe/ManweSamplesList.scala
+2
-2
public/biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/ManweTest.scala
...test/scala/nl/lumc/sasc/biopet/extensions/ManweTest.scala
+6
-0
public/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala
...n/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala
+4
-2
No files found.
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweAnnotateBed.scala
View file @
f5409cd1
...
...
@@ -19,7 +19,7 @@ class ManweAnnotateBed(val root: Configurable) extends Manwe {
@Argument
(
doc
=
"Flag whether to wait for annotation to complete on the server"
)
var
waitToComplete
:
Boolean
=
false
@Argument
(
doc
=
"annotation queries"
)
@Argument
(
doc
=
"annotation queries"
,
required
=
false
)
var
queries
:
List
[
String
]
=
Nil
def
subCommand
=
{
...
...
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweAnnotateVcf.scala
View file @
f5409cd1
...
...
@@ -19,7 +19,7 @@ class ManweAnnotateVcf(val root: Configurable) extends Manwe {
@Argument
(
doc
=
"flag whether to wait for annotation to complete"
)
var
waitToComplete
:
Boolean
=
false
@Argument
(
doc
=
"annotation queries"
)
@Argument
(
doc
=
"annotation queries"
,
required
=
false
)
var
queries
:
List
[
String
]
=
Nil
def
subCommand
=
{
...
...
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweDataSourcesAnnotate.scala
View file @
f5409cd1
...
...
@@ -11,7 +11,7 @@ class ManweDataSourcesAnnotate(val root: Configurable) extends Manwe {
@Argument
(
doc
=
"uri to data source to annotate"
)
var
uri
:
Option
[
String
]
=
_
@Argument
(
doc
=
"list of queries"
)
@Argument
(
doc
=
"list of queries"
,
required
=
false
)
var
queries
:
List
[
String
]
=
Nil
@Argument
(
doc
=
"Flag whether to wait for annotation to complete on server"
)
...
...
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesAdd.scala
View file @
f5409cd1
...
...
@@ -13,7 +13,7 @@ class ManweSamplesAdd(val root: Configurable) extends Manwe {
@Argument
(
doc
=
"the sample name"
)
var
name
:
Option
[
String
]
=
_
@Argument
(
doc
=
"the sample groups [uris]"
)
@Argument
(
doc
=
"the sample groups [uris]"
,
required
=
false
)
var
group
:
List
[
String
]
=
Nil
@Argument
(
doc
=
"pool size"
)
...
...
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesAnnotateVariations.scala
View file @
f5409cd1
...
...
@@ -13,7 +13,7 @@ class ManweSamplesAnnotateVariations(val root: Configurable) extends Manwe {
@Argument
(
doc
=
"uri to sample to annotate"
)
var
uri
:
Option
[
String
]
=
_
@Argument
(
doc
=
"Annotation queries"
)
@Argument
(
doc
=
"Annotation queries"
,
required
=
false
)
var
queries
:
List
[
String
]
=
Nil
def
subCommand
=
{
...
...
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesList.scala
View file @
f5409cd1
...
...
@@ -10,10 +10,10 @@ import org.broadinstitute.gatk.utils.commandline.{ Argument, Output }
*/
class
ManweSamplesList
(
val
root
:
Configurable
)
extends
Manwe
{
@Argument
(
doc
=
"filter by user URI"
)
@Argument
(
doc
=
"filter by user URI"
,
required
=
false
)
var
user
:
Option
[
String
]
=
None
@Argument
(
doc
=
"filter by group URI"
)
@Argument
(
doc
=
"filter by group URI"
,
required
=
false
)
var
group
:
List
[
String
]
=
Nil
var
onlyPublic
:
Boolean
=
false
...
...
public/biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/ManweTest.scala
View file @
f5409cd1
...
...
@@ -30,6 +30,8 @@ class ManweTest extends TestNGSuite with Matchers {
manwe
.
output
=
out
manwe
.
bed
=
bed
manwe
.
alreadyUploaded
=
false
manwe
.
cmd
should
equal
(
s
"manwe annotate-bed ${bed.getAbsolutePath} -c /usr/local/nonexistent.conf > ${out.getAbsolutePath}"
)
manwe
.
queries
=
List
(
"/uri/1&&/uri/2"
)
manwe
.
cmd
should
equal
(
s
"manwe annotate-bed ${bed.getAbsolutePath} -q /uri/1&&/uri/2 -c /usr/local/nonexistent.conf > ${out.getAbsolutePath}"
)
...
...
@@ -55,6 +57,8 @@ class ManweTest extends TestNGSuite with Matchers {
manwe
.
output
=
out
manwe
.
vcf
=
vcf
manwe
.
alreadyUploaded
=
false
manwe
.
cmd
should
equal
(
s
"manwe annotate-vcf ${vcf.getAbsolutePath} -c /usr/local/nonexistent.conf > ${out.getAbsolutePath}"
)
manwe
.
queries
=
List
(
"/uri/1&&/uri/2"
)
manwe
.
cmd
should
equal
(
s
"manwe annotate-vcf ${vcf.getAbsolutePath} -q /uri/1&&/uri/2 -c /usr/local/nonexistent.conf > ${out.getAbsolutePath}"
)
...
...
@@ -77,6 +81,8 @@ class ManweTest extends TestNGSuite with Matchers {
manwe
.
manweConfig
=
new
File
(
"/usr/local/nonexistent.conf"
)
manwe
.
output
=
out
manwe
.
uri
=
Some
(
"/uri/1"
)
manwe
.
cmd
should
equal
(
s
"manwe data-sources annotate /uri/1 -c /usr/local/nonexistent.conf > ${out.getAbsolutePath}"
)
manwe
.
queries
=
List
(
"/uri/1&&/uri/2"
)
manwe
.
cmd
should
equal
(
s
"manwe data-sources annotate /uri/1 -q /uri/1&&/uri/2 -c /usr/local/nonexistent.conf > ${out.getAbsolutePath}"
)
...
...
public/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala
View file @
f5409cd1
...
...
@@ -109,7 +109,7 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
val
splits
=
sampleIds
.
map
(
x
=>
{
val
view
=
new
BcftoolsView
(
this
)
view
.
input
=
vcf
view
.
output
=
swapExt
(
vcf
,
".vcf.gz"
,
s
"$x.vcf.gz"
)
view
.
output
=
swapExt
(
outputDir
,
vcf
,
".vcf.gz"
,
s
"$x.vcf.gz"
)
view
.
samples
=
List
(
x
)
view
.
minAC
=
Some
(
1
)
add
(
view
)
...
...
@@ -147,7 +147,9 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
val
annotate
=
new
ManweAnnotateVcf
(
this
)
annotate
.
vcf
=
vcf
annotate
.
queries
=
annotationQueries
if
(
annotationQueries
.
nonEmpty
)
{
annotate
.
queries
=
annotationQueries
}
annotate
.
waitToComplete
=
true
annotate
.
output
=
swapExt
(
outputDir
,
vcf
,
".vcf.gz"
,
".tmp.annot"
)
add
(
annotate
)
...
...
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