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biopet.biopet
Commits
4fb8a7b6
Commit
4fb8a7b6
authored
Apr 18, 2017
by
Peter van 't Hof
Committed by
GitHub
Apr 18, 2017
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Merge pull request #82 from biopet/Fix-BIOPET-572
Change default file name from "R1" to "sampleName - libName"
parents
0140969c
58d71f66
Changes
2
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2 changed files
with
2 additions
and
7 deletions
+2
-7
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingle.scala
...ala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingle.scala
+1
-6
gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingleTest.scala
...nl/lumc/sasc/biopet/pipelines/gears/GearsSingleTest.scala
+1
-1
No files found.
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingle.scala
View file @
4fb8a7b6
...
...
@@ -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
)
{
...
...
gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingleTest.scala
View file @
4fb8a7b6
...
...
@@ -108,7 +108,7 @@ abstract class TestGearsSingle extends TestNGSuite with Matchers {
gears
.
outputName
shouldBe
"test"
}
else
{
// in the following cases the filename should have been determined by the filename
gears
.
outputName
shouldBe
(
if
(
inputMode
==
Some
(
"bam"
))
"bamfile"
else
"R1"
)
gears
.
outputName
shouldBe
"sampleName-libName"
}
val
pipesJobs
=
gears
.
functions
.
filter
(
_
.
isInstanceOf
[
BiopetCommandLineFunction
])
...
...
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