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biopet.biopet
Commits
a2c870b2
Commit
a2c870b2
authored
Mar 20, 2017
by
Peter van 't Hof
Browse files
Adding more output files to gearssingle
parent
b118cadf
Changes
2
Hide whitespace changes
Inline
Side-by-side
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala
View file @
a2c870b2
...
...
@@ -85,8 +85,8 @@ object GearsReport extends MultisampleReportBuilder {
def
samplePage
(
sampleId
:
Int
,
args
:
Map
[
String
,
Any
])
:
ReportPage
=
{
val
krakenExecuted
=
Await
.
result
(
summary
.
getStatsSize
(
runId
,
"gearskraken"
,
"krakenreport"
,
sample
=
sampleId
,
library
=
NoLibrary
),
Duration
.
Inf
)
==
1
val
centrifugeExecuted
=
Await
.
result
(
summary
.
getStatsSize
(
runId
,
"gearscentrifuge"
,
"centrifuge_report"
,
sample
=
sampleId
,
library
=
None
),
Duration
.
Inf
)
==
1
val
qiimeClosesOtuTable
=
Await
.
result
(
summary
.
getFile
(
runId
,
"gears"
,
NoModule
,
sampleId
,
NoLibrary
,
"qiime_closed_otu_table"
),
Duration
.
Inf
)
val
qiimeOpenOtuTable
=
Await
.
result
(
summary
.
getFile
(
runId
,
"gears"
,
NoModule
,
sampleId
,
NoLibrary
,
"qiime_open_otu_table"
),
Duration
.
Inf
)
val
qiimeClosesOtuTable
=
Await
.
result
(
summary
.
getFile
(
runId
,
"gears
single
"
,
NoModule
,
sampleId
,
NoLibrary
,
"qiime_closed_otu_table"
),
Duration
.
Inf
)
val
qiimeOpenOtuTable
=
Await
.
result
(
summary
.
getFile
(
runId
,
"gears
single
"
,
NoModule
,
sampleId
,
NoLibrary
,
"qiime_open_otu_table"
),
Duration
.
Inf
)
ReportPage
((
if
(
centrifugeExecuted
)
List
(
"Centriguge analysis"
->
ReportPage
(
List
(
"Non-unique"
->
ReportPage
(
List
(),
List
(
"All mappings"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
,
Map
(
"summaryStatsTag"
->
"centrifuge_report"
)
...
...
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingle.scala
View file @
a2c870b2
...
...
@@ -150,6 +150,7 @@ class GearsSingle(val parent: Configurable) extends QScript with SummaryQScript
centrifuge
.
fastqR2
=
r2
centrifuge
.
outputName
=
outputName
add
(
centrifuge
)
outputFiles
+=
"centrifuge_output"
->
centrifuge
.
centrifugeOutput
}
qiimeRatx
foreach
{
qiimeRatx
=>
...
...
@@ -163,18 +164,21 @@ class GearsSingle(val parent: Configurable) extends QScript with SummaryQScript
qiimeClosed
.
outputDir
=
new
File
(
outputDir
,
"qiime_closed"
)
qiimeClosed
.
fastqInput
=
combinedFastq
add
(
qiimeClosed
)
outputFiles
+=
"qiime_closed_otu_table"
->
qiimeClosed
.
otuTable
}
qiimeOpen
foreach
{
qiimeOpen
=>
qiimeOpen
.
outputDir
=
new
File
(
outputDir
,
"qiime_open"
)
qiimeOpen
.
fastqInput
=
combinedFastq
add
(
qiimeOpen
)
outputFiles
+=
"qiime_open_otu_table"
->
qiimeOpen
.
otuTable
}
seqCount
.
foreach
{
seqCount
=>
seqCount
.
fastqInput
=
combinedFastq
seqCount
.
outputDir
=
new
File
(
outputDir
,
"seq_count"
)
add
(
seqCount
)
outputFiles
+=
"seq_count_count_file"
->
seqCount
.
countFile
}
addSummaryJobs
()
...
...
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