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biopet.biopet
Commits
3b55324c
Commit
3b55324c
authored
Dec 29, 2015
by
Peter van 't Hof
Browse files
Added count seqs
parent
03c15ef3
Changes
2
Hide whitespace changes
Inline
Side-by-side
public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSeqCount.scala
0 → 100644
View file @
3b55324c
package
nl.lumc.sasc.biopet.pipelines.gears
import
nl.lumc.sasc.biopet.core.
{
BiopetQScript
,
SampleLibraryTag
}
import
nl.lumc.sasc.biopet.core.summary.SummaryQScript
import
nl.lumc.sasc.biopet.extensions.tools.SageCountFastq
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.queue.QScript
/**
* Created by pjvan_thof on 12/29/15.
*/
class
GearsSeqCount
(
val
root
:
Configurable
)
extends
QScript
with
BiopetQScript
with
SampleLibraryTag
{
var
fastqInput
:
File
=
_
def
countFile
=
swapExt
(
outputDir
,
fastqInput
,
".fastq.gz"
,
".counts.txt"
)
/** Init for pipeline */
def
init
()
:
Unit
=
{
}
/** Pipeline itself */
def
biopetScript
()
:
Unit
=
{
val
seqCount
=
new
SageCountFastq
(
this
)
seqCount
.
input
=
fastqInput
seqCount
.
output
=
countFile
add
(
seqCount
)
}
}
public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingle.scala
View file @
3b55324c
...
...
@@ -44,6 +44,7 @@ class GearsSingle(val root: Configurable) extends QScript with SummaryQScript wi
lazy
val
krakenScript
=
if
(
config
(
"gears_use_kraken"
,
default
=
true
))
Some
(
new
GearsKraken
(
this
))
else
None
lazy
val
qiimeRatx
=
if
(
config
(
"gear_use_qiime_rtax"
,
default
=
false
))
Some
(
new
GearsQiimeRtax
(
this
))
else
None
lazy
val
qiimeClosed
=
if
(
config
(
"gear_use_qiime_closed"
,
default
=
false
))
Some
(
new
GearsQiimeClosed
(
this
))
else
None
lazy
val
seqCount
=
if
(
config
(
"gear_use_seq_count"
,
default
=
false
))
Some
(
new
GearsSeqCount
(
this
))
else
None
/** Executed before running the script */
def
init
()
:
Unit
=
{
...
...
@@ -137,6 +138,12 @@ class GearsSingle(val root: Configurable) extends QScript with SummaryQScript wi
//TODO: Plots
}
seqCount
.
foreach
{
seqCount
=>
seqCount
.
fastqInput
=
combinedFastq
seqCount
.
outputDir
=
new
File
(
outputDir
,
"seq_count"
)
add
(
seqCount
)
}
addSummaryJobs
()
}
...
...
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