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biopet.biopet
Commits
1e8b3c2f
Commit
1e8b3c2f
authored
Jul 24, 2017
by
Peter van 't Hof
Committed by
GitHub
Jul 24, 2017
Browse files
Merge pull request #163 from biopet/fix-BIOPET-753
Fixing summary in Basty
parents
5d3b5448
6bda10a5
Changes
2
Hide whitespace changes
Inline
Side-by-side
basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala
View file @
1e8b3c2f
...
...
@@ -21,9 +21,10 @@ package nl.lumc.sasc.biopet.pipelines.basty
import
java.io.File
import
nl.lumc.sasc.biopet.core.report.ReportBuilderExtension
import
nl.lumc.sasc.biopet.core.
{
MultiSampleQScript
,
PipelineCommand
}
import
nl.lumc.sasc.biopet.extensions.
{
Cat
,
Raxml
,
RunGubbins
}
import
nl.lumc.sasc.biopet.pipelines.shiva.Shiva
import
nl.lumc.sasc.biopet.pipelines.shiva.
{
Shiva
,
ShivaReport
}
import
nl.lumc.sasc.biopet.extensions.tools.BastyGenerateFasta
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.queue.QScript
...
...
@@ -44,6 +45,8 @@ class Basty(val parent: Configurable) extends QScript with MultiSampleQScript {
val
numBoot
:
Int
=
config
(
"boot_runs"
,
default
=
100
,
namespace
=
"raxml"
).
asInt
val
executeGubbins
:
Boolean
=
config
(
"execute_gubbins"
,
default
=
true
)
override
def
defaults
=
Map
(
"ploidy"
->
1
,
"variantcallers"
->
variantcallers
...
...
@@ -51,6 +54,13 @@ class Basty(val parent: Configurable) extends QScript with MultiSampleQScript {
lazy
val
shiva
=
new
Shiva
(
qscript
)
override
def
reportClass
:
Option
[
ReportBuilderExtension
]
=
{
val
shiva
=
new
ShivaReport
(
this
)
shiva
.
outputDir
=
new
File
(
outputDir
,
"report"
)
shiva
.
summaryDbFile
=
summaryDbFile
Some
(
shiva
)
}
def
summaryFiles
:
Map
[
String
,
File
]
=
Map
()
def
summarySettings
:
Map
[
String
,
Any
]
=
Map
(
"boot_runs"
->
numBoot
)
...
...
@@ -87,17 +97,15 @@ class Basty(val parent: Configurable) extends QScript with MultiSampleQScript {
def
init
()
{
shiva
.
outputDir
=
outputDir
shiva
.
init
()
}
def
biopetScript
()
{
shiva
.
biopetScript
()
addAll
(
shiva
.
functions
)
addSummaryQScript
(
shiva
)
add
(
shiva
)
inputFiles
:::=
shiva
.
inputFiles
addSamplesJobs
()
addSummaryJobs
()
}
def
addMultiSampleJobs
()
:
Unit
=
{
...
...
@@ -186,11 +194,13 @@ class Basty(val parent: Configurable) extends QScript with MultiSampleQScript {
raxmlBi
.
w
=
dirSufixRaxml
add
(
raxmlBi
)
val
gubbins
=
new
RunGubbins
(
this
)
gubbins
.
fastafile
=
concensusVariants
gubbins
.
startingTree
=
raxmlBi
.
getBipartitionsFile
gubbins
.
outputDirectory
=
dirSufixGubbins
add
(
gubbins
)
if
(
executeGubbins
)
{
val
gubbins
=
new
RunGubbins
(
this
)
gubbins
.
fastafile
=
concensusVariants
gubbins
.
startingTree
=
raxmlBi
.
getBipartitionsFile
gubbins
.
outputDirectory
=
dirSufixGubbins
add
(
gubbins
)
}
}
addTreeJobs
(
catVariantsSnps
.
output
,
...
...
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala
View file @
1e8b3c2f
...
...
@@ -207,15 +207,18 @@ trait SummaryQScript extends BiopetQScript { qscript: QScript =>
for
(
inputFile
<-
inputFiles
)
{
inputFile
.
md5
match
{
case
Some
(
checksum
)
=>
val
checkMd5
=
new
CheckChecksum
checkMd5
.
inputFile
=
inputFile
.
file
if
(!
SummaryQScript
.
md5sumCache
.
contains
(
inputFile
.
file
))
addChecksum
(
inputFile
.
file
)
checkMd5
.
checksumFile
=
SummaryQScript
.
md5sumCache
(
inputFile
.
file
)
checkMd5
.
checksum
=
checksum
checkMd5
.
jobOutputFile
=
new
File
(
checkMd5
.
checksumFile
.
getParentFile
,
checkMd5
.
checksumFile
.
getName
+
".check.out"
)
add
(
checkMd5
)
if
(!
SummaryQScript
.
checkChecksumCache
.
contains
(
inputFile
.
file
))
{
val
checkMd5
=
new
CheckChecksum
checkMd5
.
inputFile
=
inputFile
.
file
if
(!
SummaryQScript
.
md5sumCache
.
contains
(
inputFile
.
file
))
addChecksum
(
inputFile
.
file
)
checkMd5
.
checksumFile
=
SummaryQScript
.
md5sumCache
(
inputFile
.
file
)
checkMd5
.
checksum
=
checksum
checkMd5
.
jobOutputFile
=
new
File
(
checkMd5
.
checksumFile
.
getParentFile
,
checkMd5
.
checksumFile
.
getName
+
".check.out"
)
add
(
checkMd5
)
SummaryQScript
.
checkChecksumCache
.
add
(
inputFile
.
file
)
}
case
_
=>
}
}
...
...
@@ -238,4 +241,5 @@ object SummaryQScript {
/** Cache to have no duplicate jobs */
protected
[
summary
]
val
md5sumCache
:
mutable.Map
[
File
,
File
]
=
mutable
.
Map
()
protected
[
summary
]
val
checkChecksumCache
:
mutable.Set
[
File
]
=
mutable
.
Set
()
}
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