Skip to content
GitLab
Projects
Groups
Snippets
/
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
Mirrors
biopet.biopet
Commits
9ec465f6
Commit
9ec465f6
authored
Oct 03, 2016
by
Peter van 't Hof
Browse files
Remove nulls
parent
b8c07bd9
Changes
1
Hide whitespace changes
Inline
Side-by-side
sage/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala
View file @
9ec465f6
...
...
@@ -15,14 +15,14 @@
package
nl.lumc.sasc.biopet.pipelines.sage
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
nl.lumc.sasc.biopet.core.
{
MultiSampleQScript
,
PipelineCommand
}
import
nl.lumc.sasc.biopet.core.
{
MultiSampleQScript
,
PipelineCommand
}
import
nl.lumc.sasc.biopet.extensions.Cat
import
nl.lumc.sasc.biopet.extensions.bedtools.BedtoolsCoverage
import
nl.lumc.sasc.biopet.extensions.picard.MergeSamFiles
import
nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep
import
nl.lumc.sasc.biopet.pipelines.mapping.Mapping
import
nl.lumc.sasc.biopet.extensions.tools.SquishBed
import
nl.lumc.sasc.biopet.extensions.tools.
{
BedtoolsCoverageToCounts
,
PrefixFastq
,
SageCountFastq
,
SageCreateLibrary
,
SageCreateTagCounts
}
import
nl.lumc.sasc.biopet.extensions.tools.
{
BedtoolsCoverageToCounts
,
PrefixFastq
,
SageCountFastq
,
SageCreateLibrary
,
SageCreateTagCounts
}
import
nl.lumc.sasc.biopet.utils.Logging
import
org.broadinstitute.gatk.queue.QScript
...
...
@@ -113,17 +113,17 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
val
libraryFastqFiles
=
libraries
.
map
(
_
.
_2
.
prefixFastq
).
toList
val
bamFile
:
File
=
if
(
libraryBamfiles
.
size
==
1
)
libraryBamfiles
.
head
else
if
(
libraryBamfiles
.
size
>
1
)
{
else
{
val
mergeSamFiles
=
MergeSamFiles
(
qscript
,
libraryBamfiles
,
new
File
(
sampleDir
,
s
"$sampleId.bam"
))
qscript
.
add
(
mergeSamFiles
)
mergeSamFiles
.
output
}
else
null
}
val
fastqFile
:
File
=
if
(
libraryFastqFiles
.
size
==
1
)
libraryFastqFiles
.
head
else
if
(
libraryFastqFiles
.
size
>
1
)
{
else
{
val
cat
=
Cat
(
qscript
,
libraryFastqFiles
,
createFile
(
".fastq"
))
qscript
.
add
(
cat
)
cat
.
output
}
else
null
}
addBedtoolsCounts
(
bamFile
,
sampleId
,
sampleDir
)
addTablibCounts
(
fastqFile
,
sampleId
,
sampleDir
)
...
...
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new 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