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biopet.biopet
Commits
7e27eee9
Commit
7e27eee9
authored
Dec 17, 2015
by
Peter van 't Hof
Browse files
Adding todo's
parent
83c0d1ee
Changes
4
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public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/MergeOtuMaps.scala
View file @
7e27eee9
...
...
@@ -2,9 +2,9 @@ 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 12/10/15.
...
...
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/MergeOtuTables.scala
View file @
7e27eee9
...
...
@@ -2,9 +2,9 @@ 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.
{
Output
,
Input
}
import
org.broadinstitute.gatk.utils.commandline.
{
Output
,
Input
}
/**
* Created by pjvan_thof on 12/10/15.
...
...
@@ -21,7 +21,6 @@ class MergeOtuTables(val root: Configurable) extends BiopetCommandLineFunction w
@Output
(
required
=
true
)
var
outputFile
:
File
=
_
override
def
beforeGraph
()
:
Unit
=
{
super
.
beforeGraph
()
require
(
input
.
nonEmpty
)
...
...
public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala
View file @
7e27eee9
...
...
@@ -137,6 +137,8 @@ class Gears(val root: Configurable) extends QScript with MultiSampleQScript { qs
add
(
Ln
(
qscript
,
qiimeClosed
.
head
.
otuMap
,
_closedOtuMap
.
get
))
add
(
Ln
(
qscript
,
qiimeClosed
.
head
.
otuTable
,
_closedOtuTable
.
get
))
}
//TODO: Plots
}
else
{
_closedOtuTable
=
None
_closedOtuMap
=
None
...
...
public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingle.scala
View file @
7e27eee9
...
...
@@ -113,6 +113,8 @@ class GearsSingle(val root: Configurable) extends QScript with SummaryQScript wi
qiimeClosed
.
fastqR1
=
flexiprep
.
fastqR1Qc
qiimeClosed
.
fastqR2
=
flexiprep
.
fastqR2Qc
add
(
qiimeClosed
)
//TODO: Plots
}
addSummaryJobs
()
...
...
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