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biopet.biopet
Commits
bace55eb
Commit
bace55eb
authored
Jun 20, 2016
by
Peter van 't Hof
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Added report to qiime open reference
parent
7657016c
Changes
4
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4 changed files
with
23 additions
and
6 deletions
+23
-6
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/PickOpenReferenceOtus.scala
.../sasc/biopet/extensions/qiime/PickOpenReferenceOtus.scala
+3
-3
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala
...ain/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala
+4
-2
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsQiimeOpen.scala
.../nl/lumc/sasc/biopet/pipelines/gears/GearsQiimeOpen.scala
+0
-1
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala
...ala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala
+16
-0
No files found.
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/PickOpenReferenceOtus.scala
View file @
bace55eb
...
...
@@ -16,9 +16,9 @@ package nl.lumc.sasc.biopet.extensions.qiime
import
java.io.File
import
nl.lumc.sasc.biopet.core.
{
BiopetCommandLineFunction
,
Version
}
import
nl.lumc.sasc.biopet.core.
{
BiopetCommandLineFunction
,
Version
}
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
/**
* Created by pjvan_thof on 12/4/15.
...
...
@@ -54,7 +54,7 @@ class PickOpenReferenceOtus(val root: Configurable) extends BiopetCommandLineFun
var
minOtuSize
:
Option
[
Int
]
=
config
(
"min_otu_size"
)
var
suppressAlignAndTree
:
Boolean
=
config
(
"suppress_taxonomy_assignment"
,
default
=
false
)
def
otuTable
=
new
File
(
outputDir
,
"otu_table_mc2.biom"
)
def
otuTable
=
new
File
(
outputDir
,
"otu_table_mc2
_w_tax
.biom"
)
def
failedOtuTable
=
new
File
(
outputDir
,
"otu_table_mc2_w_tax_no_pynast_failures.biom"
)
def
otuMap
=
new
File
(
outputDir
,
"final_otu_map.txt"
)
...
...
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala
View file @
bace55eb
...
...
@@ -131,8 +131,8 @@ class Gears(val root: Configurable) extends QScript with MultiSampleQScript { qs
class
Sample
(
sampleId
:
String
)
extends
AbstractSample
(
sampleId
)
{
/**
* Factory method for Library class
*
* @param id SampleId
*
* @param id SampleId
* @return Sample class
*/
def
makeLibrary
(
id
:
String
)
:
Library
=
new
Library
(
id
)
...
...
@@ -224,6 +224,8 @@ class Gears(val root: Configurable) extends QScript with MultiSampleQScript { qs
/** File to put in the summary for thie pipeline */
def
summaryFiles
:
Map
[
String
,
File
]
=
(
qiimeOpenOtuTable
.
map
(
"qiime_open_otu_table"
->
_
)
++
qiimeOpenOtuMap
.
map
(
"qiime_open_otu_map"
->
_
)
++
qiimeClosedOtuTable
.
map
(
"qiime_closed_otu_table"
->
_
)
++
qiimeClosedOtuMap
.
map
(
"qiime_closed_otu_map"
->
_
)
).
toMap
...
...
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsQiimeOpen.scala
View file @
bace55eb
...
...
@@ -88,4 +88,3 @@ class GearsQiimeOpen(val root: Configurable) extends QScript with SummaryQScript
}
}
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala
View file @
bace55eb
...
...
@@ -40,6 +40,9 @@ object GearsReport extends MultisampleReportBuilder {
val
krakenExecuted
=
summary
.
getSampleValues
(
"gearskraken"
,
"stats"
,
"krakenreport"
).
values
.
forall
(
_
.
isDefined
)
val
qiimeClosesOtuTable
=
summary
.
getValue
(
"gears"
,
"files"
,
"pipeline"
,
"qiime_closed_otu_table"
,
"path"
)
.
map
(
x
=>
new
File
(
x
.
toString
))
val
qiimeOpenOtuTable
=
summary
.
getValue
(
"gears"
,
"files"
,
"pipeline"
,
"qiime_open_otu_table"
,
"path"
)
.
map
(
x
=>
new
File
(
x
.
toString
))
ReportPage
(
(
if
(
krakenExecuted
)
List
(
"Kraken analysis"
->
ReportPage
(
List
(),
List
(
...
...
@@ -48,6 +51,9 @@ object GearsReport extends MultisampleReportBuilder {
else
Nil
)
:::
(
if
(
qiimeClosesOtuTable
.
isDefined
)
List
(
"Qiime closed reference analysis"
->
ReportPage
(
List
(),
List
(
"Krona plot"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/qiimeKrona.ssp"
)),
Map
(
"biomFile"
->
qiimeClosesOtuTable
.
get
)))
else
Nil
)
:::
(
if
(
qiimeOpenOtuTable
.
isDefined
)
List
(
"Qiime open reference analysis"
->
ReportPage
(
List
(),
List
(
"Krona plot"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/qiimeKrona.ssp"
)),
Map
(
"biomFile"
->
qiimeOpenOtuTable
.
get
)))
else
Nil
)
:::
List
(
"Samples"
->
generateSamplesPage
(
pageArgs
))
++
Map
(
"Versions"
->
ReportPage
(
List
(),
List
(
...
...
@@ -71,6 +77,8 @@ object GearsReport extends MultisampleReportBuilder {
val
krakenExecuted
=
summary
.
getValue
(
Some
(
sampleId
),
None
,
"gearskraken"
,
"stats"
,
"krakenreport"
).
isDefined
val
qiimeClosesOtuTable
=
summary
.
getValue
(
Some
(
sampleId
),
None
,
"gearsqiimeclosed"
,
"files"
,
"pipeline"
,
"otu_table"
,
"path"
)
.
map
(
x
=>
new
File
(
x
.
toString
))
val
qiimeOpenOtuTable
=
summary
.
getValue
(
Some
(
sampleId
),
None
,
"gearsqiimeopen"
,
"files"
,
"pipeline"
,
"otu_table"
,
"path"
)
.
map
(
x
=>
new
File
(
x
.
toString
))
ReportPage
((
if
(
krakenExecuted
)
List
(
"Kraken"
->
ReportPage
(
List
(),
List
(
"Kraken analysis"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
...
...
@@ -78,6 +86,9 @@ object GearsReport extends MultisampleReportBuilder {
else
Nil
)
:::
(
if
(
qiimeClosesOtuTable
.
isDefined
)
List
(
"Qiime closed reference analysis"
->
ReportPage
(
List
(),
List
(
"Krona plot"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/qiimeKrona.ssp"
)),
Map
(
"biomFile"
->
qiimeClosesOtuTable
.
get
)))
else
Nil
)
:::
(
if
(
qiimeOpenOtuTable
.
isDefined
)
List
(
"Qiime open reference analysis"
->
ReportPage
(
List
(),
List
(
"Krona plot"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/qiimeKrona.ssp"
)),
Map
(
"biomFile"
->
qiimeOpenOtuTable
.
get
)))
else
Nil
)
:::
List
(
"Libraries"
->
generateLibraryPage
(
args
)
),
List
(
"QC reads"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"
),
...
...
@@ -91,6 +102,8 @@ object GearsReport extends MultisampleReportBuilder {
val
krakenExecuted
=
summary
.
getValue
(
Some
(
sampleId
),
Some
(
libId
),
"gearskraken"
,
"stats"
,
"krakenreport"
).
isDefined
val
qiimeClosesOtuTable
=
summary
.
getValue
(
Some
(
sampleId
),
Some
(
libId
),
"gearsqiimeclosed"
,
"files"
,
"pipeline"
,
"otu_table"
,
"path"
)
.
map
(
x
=>
new
File
(
x
.
toString
))
val
qiimeOpenOtuTable
=
summary
.
getValue
(
Some
(
sampleId
),
Some
(
libId
),
"gearsqiimeopen"
,
"files"
,
"pipeline"
,
"otu_table"
,
"path"
)
.
map
(
x
=>
new
File
(
x
.
toString
))
ReportPage
(
(
if
(
flexiprepExecuted
)
List
(
"QC"
->
FlexiprepReport
.
flexiprepPage
)
else
Nil
...
...
@@ -100,6 +113,9 @@ object GearsReport extends MultisampleReportBuilder {
else
Nil
)
:::
(
if
(
qiimeClosesOtuTable
.
isDefined
)
List
(
"Qiime closed reference analysis"
->
ReportPage
(
List
(),
List
(
"Krona plot"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/qiimeKrona.ssp"
)),
Map
(
"biomFile"
->
qiimeClosesOtuTable
.
get
)))
else
Nil
)
:::
(
if
(
qiimeOpenOtuTable
.
isDefined
)
List
(
"Qiime open reference analysis"
->
ReportPage
(
List
(),
List
(
"Krona plot"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/qiimeKrona.ssp"
)),
Map
(
"biomFile"
->
qiimeOpenOtuTable
.
get
)))
else
Nil
),
List
(
"QC reads"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"
),
"QC bases"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp"
)
...
...
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