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Mirrors
biopet.biopet
Commits
166530dc
Commit
166530dc
authored
Feb 24, 2017
by
Peter van 't Hof
Browse files
Remove old summary code and fixed dependencies for report
parent
b1d39961
Changes
32
Hide whitespace changes
Inline
Side-by-side
bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
View file @
166530dc
...
...
@@ -43,13 +43,6 @@ class BamMetrics(val parent: Configurable) extends QScript
override
def
defaults
=
Map
(
"bedtoolscoverage"
->
Map
(
"sorted"
->
true
))
/** return location of summary file */
def
summaryFile
=
(
sampleId
,
libId
)
match
{
case
(
Some
(
s
),
Some
(
l
))
=>
new
File
(
outputDir
,
s
+
"-"
+
l
+
".BamMetrics.summary.json"
)
case
(
Some
(
s
),
_
)
=>
new
File
(
outputDir
,
s
+
".BamMetrics.summary.json"
)
case
_
=>
new
File
(
outputDir
,
"BamMetrics.summary.json"
)
}
/** returns files to store in summary */
def
summaryFiles
=
Map
(
"reference"
->
referenceFasta
(),
"input_bam"
->
inputBam
)
++
...
...
basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala
View file @
166530dc
...
...
@@ -52,8 +52,6 @@ class Basty(val parent: Configurable) extends QScript with MultiSampleQScript {
lazy
val
shiva
=
new
Shiva
(
qscript
)
def
summaryFile
:
File
=
new
File
(
outputDir
,
"Basty.summary.json"
)
def
summaryFiles
:
Map
[
String
,
File
]
=
Map
()
def
summarySettings
:
Map
[
String
,
Any
]
=
Map
(
"boot_runs"
->
numBoot
)
...
...
basty/src/test/scala/nl/lumc/sasc/biopet/pipelines/basty/BastyTest.scala
View file @
166530dc
...
...
@@ -103,7 +103,6 @@ class BastyTest extends TestNGSuite with Matchers {
pipeline
.
summarySettings
.
get
(
"boot_runs"
)
shouldBe
Some
(
bootRuns
.
getOrElse
(
100
))
pipeline
.
summaryFile
shouldBe
new
File
(
BastyTest
.
outputDir
,
"Basty.summary.json"
)
pipeline
.
summaryFiles
shouldBe
Map
()
pipeline
.
samples
foreach
{
...
...
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
View file @
166530dc
...
...
@@ -90,6 +90,10 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
case
q
:
MultiSampleQScript
if
q.onlySamples.nonEmpty
&&
!q.samples.forall
(
x
=>
q.onlySamples.contains
(
x.
_
1
))
=>
logger
.
info
(
"Write report is skipped because sample flag is used"
)
case
_
=>
reportClass
.
foreach
{
report
=>
for
(
f
<-
functions
)
f
match
{
case
w
:
WriteSummary
=>
report
.
deps
:+=
w
.
jobOutputFile
case
_
=>
}
add
(
report
)
}
}
...
...
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala
View file @
166530dc
...
...
@@ -50,9 +50,6 @@ trait SummaryQScript extends BiopetQScript { qscript: QScript =>
/** File to put in the summary for thie pipeline */
def
summaryFiles
:
Map
[
String
,
File
]
/** Name of summary output file */
def
summaryFile
:
File
def
summaryDbFile
:
File
=
root
match
{
case
s
:
SummaryQScript
=>
new
File
(
s
.
outputDir
,
s
"${s.summaryName}.summary.db"
)
case
_
=>
throw
new
IllegalStateException
(
"Root should be a SummaryQScript"
)
...
...
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
View file @
166530dc
...
...
@@ -44,9 +44,6 @@ class WriteSummary(val parent: SummaryQScript) extends InProcessFunction with Co
@Input
(
doc
=
"deps"
,
required
=
false
)
var
deps
:
List
[
File
]
=
Nil
@Output
(
doc
=
"Summary output"
,
required
=
true
)
var
out
:
File
=
qscript
.
summaryFile
var
md5sum
:
Boolean
=
config
(
"summary_md5"
,
default
=
true
)
//TODO: add more checksums types
...
...
@@ -77,8 +74,6 @@ class WriteSummary(val parent: SummaryQScript) extends InProcessFunction with Co
val
pipelineId
=
Await
.
result
(
db
.
createPipeline
(
qscript
.
summaryName
,
qscript
.
summaryRunId
),
Duration
.
Inf
)
qscript
.
summarizables
.
map
(
x
=>
Await
.
result
(
db
.
createModule
(
x
.
_1
.
_1
,
qscript
.
summaryRunId
,
pipelineId
),
Duration
.
Inf
))
for
(
q
<-
qscript
.
summaryQScripts
)
deps
:+=
q
.
summaryFile
for
((
_
,
l
)
<-
qscript
.
summarizables
;
s
<-
l
)
{
deps
:::=
s
.
summaryDeps
s
match
{
...
...
@@ -91,7 +86,7 @@ class WriteSummary(val parent: SummaryQScript) extends InProcessFunction with Co
}
}
jobOutputFile
=
new
File
(
qscript
.
summaryDbFile
.
getParentFile
,
".
"
+
qscript
.
summary
DbFile
.
get
Name
.
s
tripSuffix
(
".db"
)
+
"
.out"
)
jobOutputFile
=
new
File
(
qscript
.
outputDir
,
s
".
${
qscript.summaryName
}
.s
ummary
.out"
)
}
def
createFile
(
db
:
SummaryDb
,
runId
:
Int
,
pipelineId
:
Int
,
moduleId
:
Option
[
Int
],
sampleId
:
Option
[
Int
],
libId
:
Option
[
Int
],
key
:
String
,
file
:
File
,
outputDir
:
File
)
=
{
...
...
@@ -174,100 +169,6 @@ class WriteSummary(val parent: SummaryQScript) extends InProcessFunction with Co
Some
(
db
.
createOrUpdateExecutable
(
qscript
.
summaryRunId
,
f
.
configNamespace
,
f
.
getVersion
))
case
_
=>
None
}).
flatten
.
foreach
(
Await
.
ready
(
_
,
Duration
.
Inf
))
///////////////// OLD //////////////////
for
(((
name
,
sampleId
,
libraryId
),
summarizables
)
<-
qscript
.
summarizables
;
summarizable
<-
summarizables
)
{
summarizable
.
addToQscriptSummary
(
qscript
,
name
)
}
val
pipelineMap
=
{
val
files
=
parseFiles
(
qscript
.
summaryFiles
)
val
settings
=
qscript
.
summarySettings
val
executables
:
Map
[
String
,
Any
]
=
{
def
fetchVersion
(
f
:
QFunction
)
:
Option
[(
String
,
Any
)]
=
{
f
match
{
case
f
:
BiopetJavaCommandLineFunction
with
Version
=>
Some
(
f
.
configNamespace
->
Map
(
"version"
->
f
.
getVersion
.
getOrElse
(
None
),
"java_md5"
->
BiopetCommandLineFunction
.
executableMd5Cache
.
getOrElse
(
f
.
executable
,
None
),
"java_version"
->
f
.
getJavaVersion
,
"jar_path"
->
f
.
jarFile
))
case
f
:
BiopetCommandLineFunction
with
Version
=>
Some
(
f
.
configNamespace
->
Map
(
"version"
->
f
.
getVersion
.
getOrElse
(
None
),
"md5"
->
BiopetCommandLineFunction
.
executableMd5Cache
.
getOrElse
(
f
.
executable
,
None
),
"path"
->
f
.
executable
))
case
f
:
Configurable
with
Version
=>
Some
(
f
.
configNamespace
->
Map
(
"version"
->
f
.
getVersion
.
getOrElse
(
None
)))
case
_
=>
None
}
}
(
qscript
.
functions
.
flatMap
(
fetchVersion
)
++
qscript
.
functions
.
flatMap
{
case
f
:
BiopetCommandLineFunction
=>
f
.
pipesJobs
case
_
=>
Nil
}.
flatMap
(
fetchVersion
(
_
))
).
toMap
}
val
map
=
Map
(
qscript
.
summaryName
->
Map
(
"settings"
->
settings
,
"files"
->
Map
(
"pipeline"
->
files
),
"executables"
->
executables
)
)
qscript
match
{
case
tag
:
SampleLibraryTag
=>
prefixSampleLibrary
(
map
,
tag
.
sampleId
,
tag
.
libId
)
case
q
:
MultiSampleQScript
=>
ConfigUtils
.
mergeMaps
(
Map
(
"samples"
->
q
.
samples
.
map
{
case
(
sampleName
,
sample
)
=>
sampleName
->
Map
(
qscript
.
summaryName
->
Map
(
"settings"
->
sample
.
summarySettings
,
"tags"
->
sample
.
sampleTags
),
"libraries"
->
sample
.
libraries
.
map
{
case
(
libName
,
lib
)
=>
libName
->
Map
(
qscript
.
summaryName
->
Map
(
"settings"
->
lib
.
summarySettings
,
"tags"
->
lib
.
libTags
)
)
}
)
}),
map
)
case
_
=>
map
}
}
val
jobsMap
=
(
for
(
((
name
,
sampleId
,
libraryId
),
summarizables
)
<-
qscript
.
summarizables
;
summarizable
<-
summarizables
)
yield
{
val
map
=
Map
(
qscript
.
summaryName
->
parseSummarizable
(
summarizable
,
name
))
(
prefixSampleLibrary
(
map
,
sampleId
,
libraryId
),
(
v1
:
Any
,
v2
:
Any
,
key
:
String
)
=>
summarizable
.
resolveSummaryConflict
(
v1
,
v2
,
key
))
}).
foldRight
(
pipelineMap
)((
a
,
b
)
=>
ConfigUtils
.
mergeMaps
(
a
.
_1
,
b
,
a
.
_2
))
val
combinedMap
=
//(for (qscript <- qscript.summaryQScripts) yield {
// ConfigUtils.fileToConfigMap(qscript.summaryFile)
// }).foldRight(jobsMap)((a, b) => ConfigUtils.mergeMaps(a, b)) ++
jobsMap
++
Map
(
"meta"
->
Map
(
"last_commit_hash"
->
LastCommitHash
,
"pipeline_version"
->
nl
.
lumc
.
sasc
.
biopet
.
Version
,
"pipeline_name"
->
qscript
.
summaryName
,
"output_dir"
->
qscript
.
outputDir
,
"run_name"
->
config
(
"run_name"
,
default
=
qSettings
.
runName
).
asString
,
"summary_creation"
->
System
.
currentTimeMillis
()
))
val
writer
=
new
PrintWriter
(
out
)
writer
.
println
(
ConfigUtils
.
mapToJson
(
combinedMap
).
nospaces
)
writer
.
close
()
///////////////// OLD //////////////////
}
def
prefixSampleLibrary
(
map
:
Map
[
String
,
Any
],
sampleId
:
Option
[
String
],
libraryId
:
Option
[
String
])
:
Map
[
String
,
Any
]
=
{
...
...
biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/summary/WriteSummaryTest.scala
View file @
166530dc
...
...
@@ -75,8 +75,8 @@ class WriteSummaryTest extends TestNGSuite with Matchers {
writer
.
deps
shouldBe
empty
writer
.
run
()
val
summary
=
new
Summary
(
writer
.
out
)
basicSummaryTest
(
summary
,
"test"
)
//
val summary = new Summary(writer.out)
//
basicSummaryTest(summary, "test")
}
@Test
...
...
@@ -91,9 +91,11 @@ class WriteSummaryTest extends TestNGSuite with Matchers {
writer
.
freezeFieldValues
()
writer
.
run
()
val
summary
=
new
Summary
(
writer
.
out
)
basicSummaryTest
(
summary
,
"test"
)
summary
.
getValue
(
"test2"
)
shouldBe
Some
(
"value"
)
throw
new
Exception
(
"Fix me"
)
// val summary = new Summary(writer.out)
// basicSummaryTest(summary, "test")
// summary.getValue("test2") shouldBe Some("value")
}
@Test
...
...
@@ -107,10 +109,12 @@ class WriteSummaryTest extends TestNGSuite with Matchers {
writer
.
freezeFieldValues
()
writer
.
run
()
val
summary
=
new
Summary
(
writer
.
out
)
basicSummaryTest
(
summary
,
"test"
)
summary
.
getValue
(
"test"
,
"stats"
,
"tool_1"
,
"key"
)
shouldBe
Some
(
"value"
)
summary
.
getValue
(
"test"
,
"files"
,
"tool_1"
,
"file_1"
,
"md5"
)
shouldBe
Some
(
"checksum"
)
throw
new
Exception
(
"Fix me"
)
// val summary = new Summary(writer.out)
// basicSummaryTest(summary, "test")
// summary.getValue("test", "stats", "tool_1", "key") shouldBe Some("value")
// summary.getValue("test", "files", "tool_1", "file_1", "md5") shouldBe Some("checksum")
}
@Test
...
...
@@ -125,11 +129,13 @@ class WriteSummaryTest extends TestNGSuite with Matchers {
writer
.
freezeFieldValues
()
writer
.
run
()
val
summary
=
new
Summary
(
writer
.
out
)
basicSummaryTest
(
summary
,
"test"
)
summary
.
getValue
(
"test"
,
"stats"
,
"tool_1"
,
"key"
)
shouldBe
Some
(
"value"
)
summary
.
getValue
(
"test"
,
"files"
,
"tool_1"
,
"file_1"
,
"md5"
)
shouldBe
Some
(
"checksum"
)
summary
.
getValue
(
"test"
,
"executables"
,
"java_command"
,
"version"
)
shouldBe
Some
(
"test version"
)
throw
new
Exception
(
"Fix me"
)
// val summary = new Summary(writer.out)
// basicSummaryTest(summary, "test")
// summary.getValue("test", "stats", "tool_1", "key") shouldBe Some("value")
// summary.getValue("test", "files", "tool_1", "file_1", "md5") shouldBe Some("checksum")
// summary.getValue("test", "executables", "java_command", "version") shouldBe Some("test version")
}
@Test
...
...
@@ -144,11 +150,13 @@ class WriteSummaryTest extends TestNGSuite with Matchers {
writer
.
freezeFieldValues
()
writer
.
run
()
val
summary
=
new
Summary
(
writer
.
out
)
basicSummaryTest
(
summary
,
"test"
)
summary
.
getValue
(
"test"
,
"stats"
,
"tool_1"
,
"key"
)
shouldBe
Some
(
"value"
)
summary
.
getValue
(
"test"
,
"files"
,
"tool_1"
,
"file_1"
,
"md5"
)
shouldBe
Some
(
"checksum"
)
summary
.
getValue
(
"test"
,
"executables"
,
"version_command"
,
"version"
)
shouldBe
Some
(
"test version"
)
throw
new
Exception
(
"Fix me"
)
// val summary = new Summary(writer.out)
// basicSummaryTest(summary, "test")
// summary.getValue("test", "stats", "tool_1", "key") shouldBe Some("value")
// summary.getValue("test", "files", "tool_1", "file_1", "md5") shouldBe Some("checksum")
// summary.getValue("test", "executables", "version_command", "version") shouldBe Some("test version")
}
@Test
...
...
@@ -163,10 +171,12 @@ class WriteSummaryTest extends TestNGSuite with Matchers {
writer
.
deps
shouldBe
empty
writer
.
run
()
val
summary
=
new
Summary
(
writer
.
out
)
basicSummaryTest
(
summary
,
"test"
,
sampleId
=
Some
(
"sampleName"
),
libId
=
Some
(
"libName"
))
summary
.
getValue
(
Some
(
"sampleName"
),
Some
(
"libName"
),
"test"
,
"stats"
,
"tool_1"
,
"key"
)
shouldBe
Some
(
"value"
)
summary
.
getValue
(
Some
(
"sampleName"
),
Some
(
"libName"
),
"test"
,
"files"
,
"tool_1"
,
"file_1"
,
"md5"
)
shouldBe
Some
(
"checksum"
)
throw
new
Exception
(
"Fix me"
)
// val summary = new Summary(writer.out)
// basicSummaryTest(summary, "test", sampleId = Some("sampleName"), libId = Some("libName"))
// summary.getValue(Some("sampleName"), Some("libName"), "test", "stats", "tool_1", "key") shouldBe Some("value")
// summary.getValue(Some("sampleName"), Some("libName"), "test", "files", "tool_1", "file_1", "md5") shouldBe Some("checksum")
}
@Test
...
...
@@ -181,10 +191,12 @@ class WriteSummaryTest extends TestNGSuite with Matchers {
writer
.
deps
shouldBe
empty
writer
.
run
()
val
summary
=
new
Summary
(
writer
.
out
)
basicSummaryTest
(
summary
,
"test"
,
sampleId
=
Some
(
"sampleName"
),
libId
=
None
)
summary
.
getValue
(
Some
(
"sampleName"
),
None
,
"test"
,
"stats"
,
"tool_1"
,
"key"
)
shouldBe
Some
(
"value"
)
summary
.
getValue
(
Some
(
"sampleName"
),
None
,
"test"
,
"files"
,
"tool_1"
,
"file_1"
,
"md5"
)
shouldBe
Some
(
"checksum"
)
throw
new
Exception
(
"Fix me"
)
// val summary = new Summary(writer.out)
// basicSummaryTest(summary, "test", sampleId = Some("sampleName"), libId = None)
// summary.getValue(Some("sampleName"), None, "test", "stats", "tool_1", "key") shouldBe Some("value")
// summary.getValue(Some("sampleName"), None, "test", "files", "tool_1", "file_1", "md5") shouldBe Some("checksum")
}
@Test
...
...
@@ -199,12 +211,14 @@ class WriteSummaryTest extends TestNGSuite with Matchers {
writer
.
deps
shouldBe
empty
writer
.
run
()
val
summary
=
new
Summary
(
writer
.
out
)
basicSummaryTest
(
summary
,
"test"
)
summary
.
getValue
(
"test"
,
"stats"
,
"tool_1"
,
"key"
)
shouldBe
Some
(
"value"
)
summary
.
getValue
(
"test"
,
"files"
,
"tool_1"
,
"file_1"
,
"md5"
)
shouldBe
Some
(
"checksum"
)
throw
new
Exception
(
"Fix me"
)
summary
.
getValue
(
Some
(
"sampleName"
),
Some
(
"libName"
),
"test"
)
should
not
be
None
// val summary = new Summary(writer.out)
// basicSummaryTest(summary, "test")
// summary.getValue("test", "stats", "tool_1", "key") shouldBe Some("value")
// summary.getValue("test", "files", "tool_1", "file_1", "md5") shouldBe Some("checksum")
//
// summary.getValue(Some("sampleName"), Some("libName"), "test") should not be None
}
}
...
...
carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala
View file @
166530dc
...
...
@@ -54,8 +54,6 @@ class Carp(val parent: Configurable) extends QScript with MultisampleMappingTrai
"macs2callpeak"
->
Map
(
"fileformat"
->
""
)
)
def
summaryFile
=
new
File
(
outputDir
,
"Carp.summary.json"
)
override
def
makeSample
(
id
:
String
)
=
new
Sample
(
id
)
class
Sample
(
sampleId
:
String
)
extends
super
.
Sample
(
sampleId
)
{
...
...
external-example/src/main/scala/org/example/group/pipelines/BiopetPipeline.scala
View file @
166530dc
...
...
@@ -27,9 +27,6 @@ import org.broadinstitute.gatk.queue.QScript
class
BiopetPipeline
(
val
parent
:
Configurable
)
extends
QScript
with
SummaryQScript
{
def
this
()
=
this
(
null
)
/** Only required when using [[SummaryQScript]] */
def
summaryFile
=
new
File
(
outputDir
,
"magpie.summary.json"
)
/** Only required when using [[SummaryQScript]] */
def
summaryFiles
:
Map
[
String
,
File
]
=
Map
()
...
...
external-example/src/main/scala/org/example/group/pipelines/HelloPipeline.scala
View file @
166530dc
...
...
@@ -23,9 +23,6 @@ import org.broadinstitute.gatk.queue.QScript
class
HelloPipeline
(
val
parent
:
Configurable
)
extends
QScript
with
SummaryQScript
{
def
this
()
=
this
(
null
)
/** Only required when using [[SummaryQScript]] */
def
summaryFile
=
new
File
(
outputDir
,
"hello.summary.json"
)
/** Only required when using [[SummaryQScript]] */
def
summaryFiles
:
Map
[
String
,
File
]
=
Map
()
...
...
external-example/src/main/scala/org/example/group/pipelines/MultisamplePipeline.scala
View file @
166530dc
...
...
@@ -37,8 +37,6 @@ class MultisamplePipeline(val parent: Configurable) extends QScript with MultiSa
// this code will be executed after all code of all samples is executed
}
def
summaryFile
:
File
=
new
File
(
outputDir
,
"MultisamplePipeline.summary.json"
)
//TODO: Add summary
def
summaryFiles
:
Map
[
String
,
File
]
=
Map
()
...
...
flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
View file @
166530dc
...
...
@@ -41,9 +41,6 @@ class Flexiprep(val parent: Configurable) extends QScript with SummaryQScript wi
/** Make a final fastq files, by default only when flexiprep is the main pipeline */
var
keepQcFastqFiles
:
Boolean
=
config
(
"keepQcFastqFiles"
,
default
=
parent
==
null
)
/** Location of summary file */
def
summaryFile
=
new
File
(
outputDir
,
sampleId
.
getOrElse
(
"x"
)
+
"-"
+
libId
.
getOrElse
(
"x"
)
+
".qc.summary.json"
)
/** Returns files to store in summary */
def
summaryFiles
:
Map
[
String
,
File
]
=
{
Map
(
"input_R1"
->
inputR1
,
"output_R1"
->
fastqR1Qc
)
++
...
...
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/CombineReads.scala
View file @
166530dc
...
...
@@ -95,7 +95,4 @@ class CombineReads(val parent: Configurable) extends QScript with SummaryQScript
/** File to put in the summary for thie pipeline */
def
summaryFiles
:
Map
[
String
,
File
]
=
Map
()
/** Name of summary output file */
def
summaryFile
:
File
=
new
File
(
outputDir
,
"combine_reads.summary.json"
)
}
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala
View file @
166530dc
...
...
@@ -45,9 +45,6 @@ class Gears(val parent: Configurable) extends QScript with MultiSampleQScript {
def
init
()
:
Unit
=
{
}
/** Name of summary output file */
def
summaryFile
:
File
=
new
File
(
outputDir
,
"gears.summary.json"
)
/** Pipeline itself */
def
biopetScript
()
:
Unit
=
{
addSamplesJobs
()
...
...
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsCentrifuge.scala
View file @
166530dc
...
...
@@ -77,9 +77,6 @@ class GearsCentrifuge(val parent: Configurable) extends QScript with SummaryQScr
addSummarizable
(
krakenReportJSON
,
s
"${name}_report"
)
}
/** Location of summary file */
def
summaryFile
=
new
File
(
outputDir
,
sampleId
.
getOrElse
(
"sampleName_unknown"
)
+
".centrifuge.summary.json"
)
/** Pipeline settings shown in the summary file */
def
summarySettings
:
Map
[
String
,
Any
]
=
Map
()
...
...
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsKraken.scala
View file @
166530dc
...
...
@@ -100,9 +100,6 @@ class GearsKraken(val parent: Configurable) extends QScript with SummaryQScript
addSummaryJobs
()
}
/** Location of summary file */
def
summaryFile
=
new
File
(
outputDir
,
sampleId
.
getOrElse
(
"sampleName_unknown"
)
+
".kraken.summary.json"
)
/** Pipeline settings shown in the summary file */
def
summarySettings
:
Map
[
String
,
Any
]
=
Map
()
...
...
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsQiimeClosed.scala
View file @
166530dc
...
...
@@ -77,9 +77,6 @@ class GearsQiimeClosed(val parent: Configurable) extends QScript with SummaryQSc
/** File to put in the summary for thie pipeline */
def
summaryFiles
:
Map
[
String
,
File
]
=
Map
(
"otu_table"
->
otuTable
,
"otu_map"
->
otuMap
)
/** Name of summary output file */
def
summaryFile
:
File
=
new
File
(
outputDir
,
"summary.closed_reference.json"
)
val
downSample
:
Option
[
Double
]
=
config
(
"downsample"
)
def
addDownsample
(
input
:
File
,
output
:
File
)
:
File
=
{
...
...
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsQiimeOpen.scala
View file @
166530dc
...
...
@@ -70,9 +70,6 @@ class GearsQiimeOpen(val parent: Configurable) extends QScript with SummaryQScri
/** File to put in the summary for thie pipeline */
def
summaryFiles
:
Map
[
String
,
File
]
=
Map
(
"otu_table"
->
otuTable
,
"otu_map"
->
otuMap
)
/** Name of summary output file */
def
summaryFile
:
File
=
new
File
(
outputDir
,
"summary.open_reference.json"
)
val
downSample
:
Option
[
Double
]
=
config
(
"downsample"
)
def
addDownsample
(
input
:
File
,
output
:
File
)
:
File
=
{
...
...
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingle.scala
View file @
166530dc
...
...
@@ -180,9 +180,6 @@ class GearsSingle(val parent: Configurable) extends QScript with SummaryQScript
addSummaryJobs
()
}
/** Location of summary file */
def
summaryFile
=
new
File
(
outputDir
,
sampleId
.
getOrElse
(
"sampleName_unknown"
)
+
".gears.summary.json"
)
/** Pipeline settings shown in the summary file */
def
summarySettings
:
Map
[
String
,
Any
]
=
Map
(
"skip_flexiprep"
->
skipFlexiprep
,
...
...
gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
View file @
166530dc
...
...
@@ -152,9 +152,6 @@ class Gentrap(val parent: Configurable) extends QScript
Some
(
pipeline
)
}
else
None
/** Output summary file */
def
summaryFile
:
File
=
new
File
(
outputDir
,
"gentrap.summary.json"
)
/** Files that will be listed in the summary file */
override
def
summaryFiles
:
Map
[
String
,
File
]
=
super
.
summaryFiles
++
Map
(
"annotation_refflat"
->
annotationRefFlat
()
...
...
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