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biopet.biopet
Commits
ae0a5dfd
Commit
ae0a5dfd
authored
Apr 14, 2017
by
Ruben Vorderman
Browse files
Fix outputname issue
parent
865f33cf
Changes
1
Hide whitespace changes
Inline
Side-by-side
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingle.scala
View file @
ae0a5dfd
...
...
@@ -56,12 +56,7 @@ class GearsSingle(val parent: Configurable) extends QScript with SummaryQScript
if
(
sampleId
==
null
||
sampleId
==
None
)
Logging
.
addError
(
"Missing sample ID on GearsSingle module"
)
if
(
outputName
==
null
)
{
if
(
fastqR1
.
nonEmpty
)
outputName
=
fastqR1
.
headOption
.
map
(
_
.
getName
.
stripSuffix
(
".gz"
)
.
stripSuffix
(
".fastq"
)
.
stripSuffix
(
".fq"
))
.
getOrElse
(
"noName"
)
else
outputName
=
bamFile
.
map
(
_
.
getName
.
stripSuffix
(
".bam"
)).
getOrElse
(
"noName"
)
outputName
=
sampleId
.
getOrElse
(
"noName"
)
+
libId
.
map
(
"-"
+
_
).
getOrElse
(
""
)
}
if
(
fastqR1
.
nonEmpty
)
{
...
...
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