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biopet.biopet
Commits
ebe2bb5f
Commit
ebe2bb5f
authored
Feb 16, 2015
by
Peter van 't Hof
Browse files
Added qscript wide summary jobs
parent
1c1ac1f0
Changes
1
Hide whitespace changes
Inline
Side-by-side
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala
View file @
ebe2bb5f
...
...
@@ -2,23 +2,27 @@ package nl.lumc.sasc.biopet.core.summary
import
java.io.File
import
nl.lumc.sasc.biopet.core.BiopetQScript
import
nl.lumc.sasc.biopet.core.
{
SampleLibraryTag
,
BiopetQScript
}
import
nl.lumc.sasc.biopet.extensions.Md5sum
/**
* Created by pjvan_thof on 2/14/15.
*/
trait
SummaryQScript
extends
BiopetQScript
{
trait
SummaryQScript
extends
BiopetQScript
with
Summarizable
{
/** 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
()
private
[
summary
]
var
summaryQScripts
:
List
[
SummaryQScript
]
=
Nil
var
summaryName
=
configName
def
summaryFile
:
File
def
addSummarizable
(
summarizable
:
Summarizable
,
name
:
String
)
:
Unit
=
{
//TODO: Automatic sample capture
addSummarizable
(
summarizable
,
name
,
None
,
None
)
this
match
{
case
tag
:
SampleLibraryTag
=>
addSummarizable
(
summarizable
,
name
,
tag
.
sampleId
,
tag
.
libId
)
case
_
=>
addSummarizable
(
summarizable
,
name
,
None
,
None
)
}
}
def
addSummarizable
(
summarizable
:
Summarizable
,
name
:
String
,
sampleId
:
Option
[
String
])
:
Unit
=
{
...
...
@@ -37,6 +41,8 @@ trait SummaryQScript extends BiopetQScript {
def
addSummaryJobs
:
Unit
=
{
val
writeSummary
=
new
WriteSummary
(
this
)
addSummarizable
(
this
,
summaryName
)
//Automatic checksums
for
((
_
,
summarizableList
)
<-
summarizables
;
summarizable
<-
summarizableList
;
(
_
,
file
)
<-
summarizable
.
summaryFiles
)
{
if
(
writeSummary
.
md5sum
&&
!
SummaryQScript
.
md5sumCache
.
contains
(
file
))
{
...
...
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