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biopet.biopet
Commits
73435d56
Commit
73435d56
authored
Feb 18, 2015
by
Peter van 't Hof
Browse files
Rename data to settings
parent
eb8aef93
Changes
6
Hide whitespace changes
Inline
Side-by-side
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala
View file @
73435d56
...
...
@@ -45,7 +45,7 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
def
summaryFiles
=
Map
()
def
summary
Data
=
Map
()
def
summary
Settings
=
Map
()
def
makeSample
(
id
:
String
)
=
new
Sample
(
id
)
class
Sample
(
sampleId
:
String
)
extends
AbstractSample
(
sampleId
)
{
...
...
public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
View file @
73435d56
...
...
@@ -49,7 +49,7 @@ class BamMetrics(val root: Configurable) extends QScript with SummaryQScript wit
def
summaryFiles
=
Map
(
"input_bam"
->
inputBam
)
def
summary
Data
=
Map
()
def
summary
Settings
=
Map
()
def
init
()
{
if
(
config
.
contains
(
"target_bed"
))
{
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala
View file @
73435d56
...
...
@@ -2,13 +2,15 @@ package nl.lumc.sasc.biopet.core.summary
import
java.io.File
import
nl.lumc.sasc.biopet.core.
{
SampleLibraryTag
,
BiopetQScript
}
import
nl.lumc.sasc.biopet.core.
{
BiopetCommandLineFunctionTrait
,
BiopetCommandLineFunction
,
SampleLibraryTag
,
BiopetQScript
}
import
nl.lumc.sasc.biopet.extensions.Md5sum
import
scala.collection.mutable
/**
* Created by pjvan_thof on 2/14/15.
*/
trait
SummaryQScript
extends
BiopetQScript
with
Summarizable
{
trait
SummaryQScript
extends
BiopetQScript
{
/** Key is sample/library, None is sample or library is not applicable */
private
[
summary
]
var
summarizables
:
Map
[(
String
,
Option
[
String
]
,
Option
[
String
])
,
List
[
Summarizable
]]
=
Map
()
...
...
@@ -16,6 +18,10 @@ trait SummaryQScript extends BiopetQScript with Summarizable {
var
summaryName
=
configName
def
summarySettings
:
Map
[
String
,
Any
]
def
summaryFiles
:
Map
[
String
,
File
]
def
summaryFile
:
File
def
addSummarizable
(
summarizable
:
Summarizable
,
name
:
String
)
:
Unit
=
{
...
...
@@ -41,10 +47,7 @@ trait SummaryQScript extends BiopetQScript with Summarizable {
def
addSummaryJobs
:
Unit
=
{
val
writeSummary
=
new
WriteSummary
(
this
)
addSummarizable
(
this
,
"pipeline"
)
//Automatic checksums
for
((
_
,
summarizableList
)
<-
summarizables
;
summarizable
<-
summarizableList
;
(
_
,
file
)
<-
summarizable
.
summaryFiles
)
{
def
addChecksum
(
file
:
File
)
:
Unit
=
{
if
(
writeSummary
.
md5sum
&&
!
SummaryQScript
.
md5sumCache
.
contains
(
file
))
{
val
md5sum
=
Md5sum
(
this
,
file
)
writeSummary
.
deps
:+=
md5sum
.
output
...
...
@@ -54,8 +57,28 @@ trait SummaryQScript extends BiopetQScript with Summarizable {
//TODO: add more checksums types
}
//Automatic checksums
for
((
_
,
summarizableList
)
<-
summarizables
;
summarizable
<-
summarizableList
;
(
_
,
file
)
<-
summarizable
.
summaryFiles
)
addChecksum
(
file
)
for
((
_
,
sl
)
<-
summarizables
)
{
for
(
s
<-
sl
)
{
s
match
{
case
c
:
BiopetCommandLineFunctionTrait
=>
{
executables
+=
c
.
configName
->
(
new
File
(
c
.
executable
),
c
.
getVersion
)
}
case
_
=>
}
}
}
for
((
_
,
file
)
<-
this
.
summaryFiles
)
addChecksum
(
file
)
add
(
writeSummary
)
}
protected
[
summary
]
val
executables
:
mutable.Map
[
String
,
(
File
,
String
)]
=
mutable
.
Map
()
}
object
SummaryQScript
{
...
...
public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala
View file @
73435d56
...
...
@@ -47,7 +47,7 @@ class Carp(val root: Configurable) extends QScript with MultiSampleQScript with
def
summaryFiles
=
Map
()
def
summary
Data
=
Map
()
def
summary
Settings
=
Map
()
def
makeSample
(
id
:
String
)
=
new
Sample
(
id
)
class
Sample
(
sampleId
:
String
)
extends
AbstractSample
(
sampleId
)
{
...
...
public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
View file @
73435d56
...
...
@@ -48,7 +48,7 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
(
if
(
paired
)
Map
(
"input_R2"
->
input_R2
.
get
,
"output_R2"
->
outputFiles
(
"output_R2_gzip"
))
else
Map
())
}
def
summary
Data
=
Map
(
"skip_trim"
->
skipTrim
,
"skip_clip"
->
skipClip
,
"paired"
->
paired
)
def
summary
Settings
=
Map
(
"skip_trim"
->
skipTrim
,
"skip_clip"
->
skipClip
,
"paired"
->
paired
)
var
paired
:
Boolean
=
input_R2
.
isDefined
var
R1_ext
:
String
=
_
...
...
@@ -136,6 +136,7 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
val
seqtkSeq_R1
=
SeqtkSeq
(
this
,
R1
,
swapExt
(
outDir
,
R1
,
R1_ext
,
".sanger"
+
R1_ext
),
fastqc_R1
)
seqtkSeq_R1
.
isIntermediate
=
true
add
(
seqtkSeq_R1
)
addSummarizable
(
seqtkSeq_R1
,
"seqtkSeq_R1"
)
R1
=
seqtkSeq_R1
.
output
deps
::=
R1
...
...
@@ -143,6 +144,7 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
val
seqtkSeq_R2
=
SeqtkSeq
(
this
,
R2
,
swapExt
(
outDir
,
R2
,
R2_ext
,
".sanger"
+
R2_ext
),
fastqc_R2
)
seqtkSeq_R2
.
isIntermediate
=
true
add
(
seqtkSeq_R2
)
addSummarizable
(
seqtkSeq_R2
,
"seqtkSeq_R2"
)
R2
=
seqtkSeq_R2
.
output
deps
::=
R2
}
...
...
public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
View file @
73435d56
...
...
@@ -96,7 +96,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
def
summaryFiles
=
Map
()
def
summary
Data
=
Map
()
def
summary
Settings
=
Map
()
def
init
()
{
require
(
outputDir
!=
null
,
"Missing output directory on mapping module"
)
...
...
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