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biopet.biopet
Commits
3c73be57
Commit
3c73be57
authored
Jan 05, 2017
by
Peter van 't Hof
Browse files
Change from error to warning
parent
86ecb782
Changes
1
Hide whitespace changes
Inline
Side-by-side
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
View file @
3c73be57
...
...
@@ -153,8 +153,8 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
require
(
inputR1
!=
null
,
"Missing inputR1 on mapping module"
)
require
(
sampleId
.
isDefined
,
"Missing sample ID on mapping module"
)
require
(
libId
.
isDefined
,
"Missing library ID on mapping module"
)
if
(
inputR1
.
exists
()
&&
inputR1
.
length
()
==
0
)
L
ogg
ing
.
addError
(
s
"Input R1 is a empty file: $inputR1"
)
inputR2
.
foreach
(
r
=>
if
(
r
.
exists
()
&&
r
.
length
()
==
0
)
L
ogg
ing
.
addError
(
s
"Input R2 is a empty file: $r"
))
if
(
inputR1
.
exists
()
&&
inputR1
.
length
()
==
0
)
l
ogg
er
.
warn
(
s
"Input R1 is a empty file: $inputR1"
)
inputR2
.
foreach
(
r
=>
if
(
r
.
exists
()
&&
r
.
length
()
==
0
)
l
ogg
er
.
warn
(
s
"Input R2 is a empty file: $r"
))
inputFiles
:+=
new
InputFile
(
inputR1
)
inputR2
.
foreach
(
inputFiles
:+=
new
InputFile
(
_
))
...
...
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