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biopet.biopet
Commits
94d9ba32
Commit
94d9ba32
authored
Sep 08, 2015
by
Peter van 't Hof
Browse files
Switch seqstat to init jobs
parent
37e92018
Changes
1
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Inline
Side-by-side
public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
View file @
94d9ba32
...
...
@@ -19,7 +19,7 @@ import nl.lumc.sasc.biopet.core.config.Configurable
import
nl.lumc.sasc.biopet.core.summary.SummaryQScript
import
nl.lumc.sasc.biopet.core.
{
PipelineCommand
,
SampleLibraryTag
}
import
nl.lumc.sasc.biopet.extensions._
import
nl.lumc.sasc.biopet.tools.
{
FastqSync
,
SeqStat
}
import
nl.lumc.sasc.biopet.tools.
{
SeqStat
,
FastqSync
}
import
org.broadinstitute.gatk.queue.QScript
class
Flexiprep
(
val
root
:
Configurable
)
extends
QScript
with
SummaryQScript
with
SampleLibraryTag
{
...
...
@@ -131,6 +131,18 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
addSummarizable
(
fastqc_R2
,
"fastqc_R2"
)
outputFiles
+=
(
"fastqc_R2"
->
fastqc_R2
.
output
)
}
val
seqstat_R1
=
SeqStat
(
this
,
input_R1
,
outputDir
)
seqstat_R1
.
isIntermediate
=
true
add
(
seqstat_R1
)
addSummarizable
(
seqstat_R1
,
"seqstat_R1"
)
if
(
paired
)
{
val
seqstat_R2
=
SeqStat
(
this
,
input_R2
.
get
,
outputDir
)
seqstat_R2
.
isIntermediate
=
true
add
(
seqstat_R2
)
addSummarizable
(
seqstat_R2
,
"seqstat_R2"
)
}
}
//TODO: Refactor need to combine all this functions
...
...
@@ -174,20 +186,6 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
deps_R2
::=
R2
.
get
}
val
seqstat_R1
=
SeqStat
(
this
,
R1
,
outDir
)
seqstat_R1
.
isIntermediate
=
true
seqstat_R1
.
deps
=
deps_R1
add
(
seqstat_R1
)
addSummarizable
(
seqstat_R1
,
"seqstat_R1"
)
if
(
paired
)
{
val
seqstat_R2
=
SeqStat
(
this
,
R2
.
get
,
outDir
)
seqstat_R2
.
isIntermediate
=
true
seqstat_R2
.
deps
=
deps_R2
add
(
seqstat_R2
)
addSummarizable
(
seqstat_R2
,
"seqstat_R2"
)
}
if
(!
skipClip
)
{
// Adapter clipping
val
cutadapt_R1
=
Cutadapt
(
this
,
R1
,
swapExt
(
outDir
,
R1
,
R1_ext
,
".clip"
+
R1_ext
))
...
...
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