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biopet.biopet
Commits
8242e484
Commit
8242e484
authored
Dec 02, 2016
by
Peter van 't Hof
Browse files
Added intermendiate tags
parent
0efd042b
Changes
4
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Inline
Side-by-side
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/CombineReads.scala
View file @
8242e484
...
...
@@ -54,12 +54,14 @@ class CombineReads(val root: Configurable) extends QScript with SummaryQScript w
swapExt
(
outputDir
,
flash
.
notCombinedR2
,
".fastq.gz"
,
".clip.fastq.gz"
)
else
flash
.
notCombinedR2
val
keepFastaqFiles
:
Boolean
=
config
(
"keep_fastq_files"
,
default
=
false
)
/** Pipeline itself */
def
biopetScript
()
:
Unit
=
{
flash
.
outputDirectory
=
new
File
(
outputDir
,
"flash"
)
flash
.
fastqR1
=
fastqR1
flash
.
fastqR2
=
fastqR2
flash
.
isIntermediate
=
(
forwardPrimers
:::
reversePrimers
).
nonEmpty
flash
.
isIntermediate
=
!
keepFastaqFiles
||
(
forwardPrimers
:::
reversePrimers
).
nonEmpty
add
(
flash
)
if
((
forwardPrimers
:::
reversePrimers
).
nonEmpty
)
{
...
...
@@ -67,6 +69,7 @@ class CombineReads(val root: Configurable) extends QScript with SummaryQScript w
cutadapt
.
fastqInput
=
flash
.
combinedFastq
cutadapt
.
fastqOutput
=
this
.
combinedFastq
cutadapt
.
statsOutput
=
swapExt
(
outputDir
,
cutadapt
.
fastqOutput
,
".fastq.gz"
,
".stats"
)
cutadapt
.
isIntermediate
=
!
keepFastaqFiles
(
forwardPrimers
:::
reversePrimers
).
foreach
(
cutadapt
.
anywhere
+=
_
)
add
(
cutadapt
)
addSummarizable
(
cutadapt
,
"cutadapt"
)
...
...
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsQiimeClosed.scala
View file @
8242e484
...
...
@@ -58,6 +58,7 @@ class GearsQiimeClosed(val root: Configurable) extends QScript with SummaryQScri
splitLib
.
input
:+=
fastqInput
splitLib
.
outputDir
=
new
File
(
outputDir
,
"split_libraries_fastq"
)
sampleId
.
foreach
(
splitLib
.
sampleIds
:+=
_
.
replaceAll
(
"_"
,
"-"
))
splitLib
.
isIntermediate
=
true
add
(
splitLib
)
val
closedReference
=
new
PickClosedReferenceOtus
(
this
)
...
...
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsQiimeOpen.scala
View file @
8242e484
...
...
@@ -51,6 +51,7 @@ class GearsQiimeOpen(val root: Configurable) extends QScript with SummaryQScript
splitLib
.
input
:+=
fastqInput
splitLib
.
outputDir
=
new
File
(
outputDir
,
"split_libraries_fastq"
)
sampleId
.
foreach
(
splitLib
.
sampleIds
:+=
_
.
replaceAll
(
"_"
,
"-"
))
splitLib
.
isIntermediate
=
true
add
(
splitLib
)
val
openReference
=
new
PickOpenReferenceOtus
(
this
)
...
...
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
View file @
8242e484
...
...
@@ -19,11 +19,11 @@ import java.util.Date
import
nl.lumc.sasc.biopet.core._
import
nl.lumc.sasc.biopet.core.summary.SummaryQScript
import
nl.lumc.sasc.biopet.extensions.bowtie.
{
Bowtie
,
Bowtie2
}
import
nl.lumc.sasc.biopet.extensions.bwa.
{
BwaAln
,
BwaMem
,
BwaSampe
,
BwaSamse
}
import
nl.lumc.sasc.biopet.extensions.bowtie.
{
Bowtie
,
Bowtie2
}
import
nl.lumc.sasc.biopet.extensions.bwa.
{
BwaAln
,
BwaMem
,
BwaSampe
,
BwaSamse
}
import
nl.lumc.sasc.biopet.extensions.gmap.Gsnap
import
nl.lumc.sasc.biopet.extensions.hisat.Hisat2
import
nl.lumc.sasc.biopet.extensions.picard.
{
AddOrReplaceReadGroups
,
MarkDuplicates
,
MergeSamFiles
,
ReorderSam
,
SortSam
}
import
nl.lumc.sasc.biopet.extensions.picard.
{
AddOrReplaceReadGroups
,
MarkDuplicates
,
MergeSamFiles
,
ReorderSam
,
SortSam
}
import
nl.lumc.sasc.biopet.extensions.tools.FastqSplitter
import
nl.lumc.sasc.biopet.extensions._
import
nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics
...
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