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biopet.biopet
Commits
2404e328
Commit
2404e328
authored
Feb 16, 2015
by
Peter van 't Hof
Browse files
Add summary framework to Carp
parent
d523db6c
Changes
1
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Inline
Side-by-side
public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala
View file @
2404e328
...
...
@@ -17,6 +17,7 @@ package nl.lumc.sasc.biopet.pipelines.carp
import
java.io.File
import
nl.lumc.sasc.biopet.core.summary.SummaryQScript
import
nl.lumc.sasc.biopet.extensions.Ln
import
nl.lumc.sasc.biopet.extensions.macs2.Macs2CallPeak
import
nl.lumc.sasc.biopet.extensions.picard.MergeSamFiles
...
...
@@ -34,7 +35,7 @@ import nl.lumc.sasc.biopet.pipelines.mapping.Mapping
* Chip-Seq analysis pipeline
* This pipeline performs QC,mapping and peak calling
*/
class
Carp
(
val
root
:
Configurable
)
extends
QScript
with
MultiSampleQScript
{
class
Carp
(
val
root
:
Configurable
)
extends
QScript
with
MultiSampleQScript
with
SummaryQScript
{
qscript
=>
def
this
()
=
this
(
null
)
...
...
@@ -42,25 +43,32 @@ class Carp(val root: Configurable) extends QScript with MultiSampleQScript {
"mapping"
->
Map
(
"skip_markduplicates"
->
true
,
"aligner"
->
"bwa"
)
),
super
.
defaults
)
def
summaryFile
=
new
File
(
outputDir
,
"Carp.summary.json"
)
def
summaryFiles
=
Map
()
def
summaryData
=
Map
()
def
makeSample
(
id
:
String
)
=
new
Sample
(
id
)
class
Sample
(
sampleId
:
String
)
extends
AbstractSample
(
sampleId
)
{
def
makeLibrary
(
id
:
String
)
=
new
Library
(
id
)
class
Library
(
libId
:
String
)
extends
AbstractLibrary
(
libId
)
{
val
mapping
=
new
Mapping
(
qscript
)
mapping
.
libId
=
Some
(
libId
)
mapping
.
sampleId
=
Some
(
sampleId
)
mapping
.
outputDir
=
libDir
def
addJobs
()
:
Unit
=
{
if
(
config
.
contains
(
"R1"
))
{
mapping
.
input_R1
=
config
(
"R1"
)
if
(
config
.
contains
(
"R2"
))
mapping
.
input_R2
=
config
(
"R2"
)
mapping
.
libId
=
Some
(
libId
)
mapping
.
sampleId
=
Some
(
sampleId
)
mapping
.
outputDir
=
libDir
mapping
.
init
mapping
.
biopetScript
addAll
(
mapping
.
functions
)
}
else
logger
.
error
(
"Sample: "
+
sampleId
+
": No R1 found for library: "
+
libId
)
addSummaryQScript
(
mapping
)
}
}
...
...
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