Skip to content
GitLab
Menu
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
657d8684
Commit
657d8684
authored
Jun 28, 2015
by
bow
Browse files
Use absolute path for tophat fix output
parent
a0e4262d
Changes
1
Hide whitespace changes
Inline
Side-by-side
public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
View file @
657d8684
...
...
@@ -368,12 +368,12 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
val
fixedUnmapped
=
new
File
(
tophat
.
output_dir
,
"unmapped_fixup.sam"
)
val
fixer
=
new
TophatRecondition
(
this
)
fixer
.
inputBam
=
tophat
.
outputAcceptedHits
fixer
.
outputSam
=
fixedUnmapped
fixer
.
outputSam
=
fixedUnmapped
.
getAbsoluteFile
fixer
.
isIntermediate
=
true
add
(
fixer
)
// sort fixed SAM file
val
sorter
=
SortSam
(
this
,
fixer
.
outputSam
,
swapExt
(
fixer
.
outputSam
,
".sam"
,
"
.sorted.bam"
))
val
sorter
=
SortSam
(
this
,
fixer
.
outputSam
,
new
File
(
tophat
.
output_dir
,
"unmapped_fixup
.sorted.bam"
))
sorter
.
sortOrder
=
"coordinate"
sorter
.
isIntermediate
=
true
add
(
sorter
)
...
...
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