Skip to content
GitLab
Projects
Groups
Snippets
Help
Loading...
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
B
biopet.biopet
Project overview
Project overview
Details
Activity
Releases
Repository
Repository
Files
Commits
Branches
Tags
Contributors
Graph
Compare
CI / CD
CI / CD
Pipelines
Jobs
Schedules
Operations
Operations
Environments
Analytics
Analytics
CI / CD
Repository
Value Stream
Members
Members
Collapse sidebar
Close sidebar
Activity
Graph
Jobs
Commits
Open sidebar
Mirrors
biopet.biopet
Commits
8242e484
Commit
8242e484
authored
Dec 02, 2016
by
Peter van 't Hof
Browse files
Options
Browse Files
Download
Email Patches
Plain Diff
Added intermendiate tags
parent
0efd042b
Changes
4
Hide whitespace changes
Inline
Side-by-side
Showing
4 changed files
with
9 additions
and
4 deletions
+9
-4
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/CombineReads.scala
...la/nl/lumc/sasc/biopet/pipelines/gears/CombineReads.scala
+4
-1
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsQiimeClosed.scala
...l/lumc/sasc/biopet/pipelines/gears/GearsQiimeClosed.scala
+1
-0
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsQiimeOpen.scala
.../nl/lumc/sasc/biopet/pipelines/gears/GearsQiimeOpen.scala
+1
-0
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
...scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
+3
-3
No files found.
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
...
...
Write
Preview
Markdown
is supported
0%
Try again
or
attach a new file
.
Attach a file
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment