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biopet.biopet
Commits
ad4b957a
Commit
ad4b957a
authored
Oct 27, 2015
by
Peter van 't Hof
Browse files
Added more settings to the summary
parent
f1011497
Changes
2
Hide whitespace changes
Inline
Side-by-side
public/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/BastyTrait.scala
View file @
ad4b957a
...
...
@@ -180,7 +180,7 @@ trait BastyTrait extends MultiSampleQScript {
snpsOnly
:
Boolean
=
false
)
:
FastaOutput
=
{
val
bastyGenerateFasta
=
new
BastyGenerateFasta
(
this
)
bastyGenerateFasta
.
outputName
=
if
(
outputName
!=
null
)
outputName
else
sampleName
bastyGenerateFasta
.
inputVcf
=
shiva
.
v
ariantCalling
.
get
.
finalFile
bastyGenerateFasta
.
inputVcf
=
shiva
.
multisampleV
ariantCalling
.
get
.
finalFile
if
(
shiva
.
samples
.
contains
(
sampleName
))
{
bastyGenerateFasta
.
bamFile
=
shiva
.
samples
(
sampleName
).
preProcessBam
.
get
}
...
...
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala
View file @
ad4b957a
...
...
@@ -84,6 +84,9 @@ trait ShivaTrait extends MultiSampleQScript with Reference {
/** Method to make a library */
def
makeLibrary
(
id
:
String
)
=
new
Library
(
id
)
/** Sample specific settings */
override
def
summarySettings
=
Map
(
"single_sample_variantcalling"
->
variantcalling
.
isDefined
)
/** Class to generate jobs for a library */
class
Library
(
libId
:
String
)
extends
AbstractLibrary
(
libId
)
{
/** Library specific files to add to the summary */
...
...
@@ -101,6 +104,9 @@ trait ShivaTrait extends MultiSampleQScript with Reference {
/** Method to execute library preprocess */
def
preProcess
(
input
:
File
)
:
Option
[
File
]
=
None
/** Library specific settings */
override
def
summarySettings
=
Map
(
"library_variantcalling"
->
variantcalling
.
isDefined
)
/** Method to make the mapping submodule */
def
makeMapping
=
{
val
mapping
=
new
Mapping
(
qscript
)
...
...
@@ -280,7 +286,7 @@ trait ShivaTrait extends MultiSampleQScript with Reference {
}
}
lazy
val
v
ariantCalling
=
if
(
config
(
"multisample_variantcalling"
,
default
=
true
).
asBoolean
)
{
lazy
val
multisampleV
ariantCalling
=
if
(
config
(
"multisample_variantcalling"
,
default
=
true
).
asBoolean
)
{
Some
(
makeVariantcalling
(
multisample
=
true
))
}
else
None
...
...
@@ -288,9 +294,14 @@ trait ShivaTrait extends MultiSampleQScript with Reference {
Some
(
new
ShivaSvCalling
(
this
))
}
else
None
lazy
val
annotation
=
if
(
multisampleVariantCalling
.
isDefined
&&
config
(
"annotation"
,
default
=
false
).
asBoolean
)
{
Some
(
new
Toucan
(
this
))
}
else
None
/** This will add the mutisample variantcalling */
def
addMultiSampleJobs
()
:
Unit
=
{
v
ariantCalling
.
foreach
(
vc
=>
{
multisampleV
ariantCalling
.
foreach
(
vc
=>
{
vc
.
outputDir
=
new
File
(
outputDir
,
"variantcalling"
)
vc
.
inputBams
=
samples
.
flatMap
(
_
.
_2
.
preProcessBam
).
toList
vc
.
init
()
...
...
@@ -298,8 +309,7 @@ trait ShivaTrait extends MultiSampleQScript with Reference {
addAll
(
vc
.
functions
)
addSummaryQScript
(
vc
)
if
(
config
(
"annotation"
,
default
=
false
).
asBoolean
)
{
val
toucan
=
new
Toucan
(
this
)
annotation
.
foreach
{
toucan
=>
toucan
.
outputDir
=
new
File
(
outputDir
,
"annotation"
)
toucan
.
inputVCF
=
vc
.
finalFile
toucan
.
init
()
...
...
@@ -330,7 +340,10 @@ trait ShivaTrait extends MultiSampleQScript with Reference {
Map
(
"reference"
->
referenceSummary
,
"regions_of_interest"
->
roiBedFiles
.
map
(
_
.
getName
.
stripSuffix
(
".bed"
)),
"amplicon_bed"
->
ampliconBedFile
.
map
(
_
.
getName
.
stripSuffix
(
".bed"
))
"amplicon_bed"
->
ampliconBedFile
.
map
(
_
.
getName
.
stripSuffix
(
".bed"
)),
"annotation"
->
annotation
.
isDefined
,
"multisample_variantcalling"
->
multisampleVariantCalling
.
isDefined
,
"sv_calling"
->
svCalling
.
isDefined
)
}
...
...
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