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biopet.biopet
Commits
1f620a44
Commit
1f620a44
authored
Feb 17, 2015
by
Peter van 't Hof
Browse files
Make all module within one qscript
parent
e193f1b6
Changes
2
Hide whitespace changes
Inline
Side-by-side
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala
View file @
1f620a44
...
...
@@ -41,7 +41,7 @@ trait SummaryQScript extends BiopetQScript with Summarizable {
def
addSummaryJobs
:
Unit
=
{
val
writeSummary
=
new
WriteSummary
(
this
)
addSummarizable
(
this
,
summaryName
)
addSummarizable
(
this
,
"pipeline"
)
//Automatic checksums
for
((
_
,
summarizableList
)
<-
summarizables
;
summarizable
<-
summarizableList
;
(
_
,
file
)
<-
summarizable
.
summaryFiles
)
{
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
View file @
1f620a44
...
...
@@ -19,20 +19,20 @@ class WriteSummary(val root: Configurable) extends InProcessFunction with Config
require
(
root
.
isInstanceOf
[
SummaryQScript
],
"root is not a SummaryQScript"
)
val
s
ummaryQS
cript
=
root
.
asInstanceOf
[
SummaryQScript
]
val
q
script
=
root
.
asInstanceOf
[
SummaryQScript
]
@Input
(
doc
=
"deps"
,
required
=
false
)
var
deps
:
List
[
File
]
=
Nil
@Output
(
doc
=
"Summary output"
,
required
=
true
)
var
out
:
File
=
s
ummaryQS
cript
.
summaryFile
var
out
:
File
=
q
script
.
summaryFile
var
md5sum
:
Boolean
=
config
(
"summary_md5"
,
default
=
true
)
//TODO: add more checksums types
override
def
freezeFieldValues
()
:
Unit
=
{
for
(
q
<-
s
ummaryQS
cript
.
summaryQScripts
)
deps
:+=
q
.
summaryFile
for
((
_
,
l
)
<-
s
ummaryQS
cript
.
summarizables
;
s
<-
l
)
s
match
{
for
(
q
<-
q
script
.
summaryQScripts
)
deps
:+=
q
.
summaryFile
for
((
_
,
l
)
<-
q
script
.
summarizables
;
s
<-
l
)
s
match
{
case
f
:
QFunction
=>
deps
:+=
f
.
firstOutput
case
_
=>
}
...
...
@@ -44,10 +44,10 @@ class WriteSummary(val root: Configurable) extends InProcessFunction with Config
def
run
()
:
Unit
=
{
val
map
=
(
for
(
((
name
,
sampleId
,
libraryId
),
summarizables
)
<-
s
ummaryQS
cript
.
summarizables
;
((
name
,
sampleId
,
libraryId
),
summarizables
)
<-
q
script
.
summarizables
;
summarizable
<-
summarizables
)
yield
{
val
map
=
Map
(
name
->
parseSummarizable
(
summarizable
))
val
map
=
Map
(
qscript
.
summaryName
->
Map
(
name
->
parseSummarizable
(
summarizable
))
)
(
sampleId
match
{
case
Some
(
sampleId
)
=>
Map
(
"samples"
->
Map
(
sampleId
->
(
libraryId
match
{
...
...
@@ -58,7 +58,7 @@ class WriteSummary(val root: Configurable) extends InProcessFunction with Config
},
(
v1
:
Any
,
v2
:
Any
,
key
:
String
)
=>
summarizable
.
resolveSummaryConflict
(
v1
,
v2
,
key
))
}).
foldRight
(
Map
[
String
,
Any
]())((
a
,
b
)
=>
ConfigUtils
.
mergeMaps
(
a
.
_1
,
b
,
a
.
_2
))
val
combinedMap
=
(
for
(
qscript
<-
s
ummaryQS
cript
.
summaryQScripts
)
yield
{
val
combinedMap
=
(
for
(
qscript
<-
q
script
.
summaryQScripts
)
yield
{
ConfigUtils
.
fileToConfigMap
(
qscript
.
summaryFile
)
}).
foldRight
(
map
)((
a
,
b
)
=>
ConfigUtils
.
mergeMaps
(
a
,
b
))
...
...
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