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biopet.biopet
Commits
86ecb782
Commit
86ecb782
authored
Jan 05, 2017
by
Peter van 't Hof
Browse files
Added a check on empty files
parent
24a1b29e
Changes
1
Hide whitespace changes
Inline
Side-by-side
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
View file @
86ecb782
...
...
@@ -19,11 +19,11 @@ import java.util.Date
import
nl.lumc.sasc.biopet.core._
import
nl.lumc.sasc.biopet.core.summary.SummaryQScript
import
nl.lumc.sasc.biopet.extensions.bowtie.
{
Bowtie
,
Bowtie2
}
import
nl.lumc.sasc.biopet.extensions.bwa.
{
BwaAln
,
BwaMem
,
BwaSampe
,
BwaSamse
}
import
nl.lumc.sasc.biopet.extensions.bowtie.
{
Bowtie
,
Bowtie2
}
import
nl.lumc.sasc.biopet.extensions.bwa.
{
BwaAln
,
BwaMem
,
BwaSampe
,
BwaSamse
}
import
nl.lumc.sasc.biopet.extensions.gmap.Gsnap
import
nl.lumc.sasc.biopet.extensions.hisat.Hisat2
import
nl.lumc.sasc.biopet.extensions.picard.
{
AddOrReplaceReadGroups
,
MarkDuplicates
,
MergeSamFiles
,
ReorderSam
,
SortSam
}
import
nl.lumc.sasc.biopet.extensions.picard.
{
AddOrReplaceReadGroups
,
MarkDuplicates
,
MergeSamFiles
,
ReorderSam
,
SortSam
}
import
nl.lumc.sasc.biopet.extensions.tools.FastqSplitter
import
nl.lumc.sasc.biopet.extensions._
import
nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics
...
...
@@ -31,7 +31,7 @@ import nl.lumc.sasc.biopet.pipelines.bamtobigwig.Bam2Wig
import
nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep
import
nl.lumc.sasc.biopet.pipelines.gears.GearsSingle
import
nl.lumc.sasc.biopet.pipelines.mapping.scripts.TophatRecondition
import
nl.lumc.sasc.biopet.utils.textToSize
import
nl.lumc.sasc.biopet.utils.
{
Logging
,
textToSize
}
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.queue.QScript
...
...
@@ -150,9 +150,11 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
/** Will be executed before script */
def
init
()
{
require
(
outputDir
!=
null
,
"Missing output directory on mapping module"
)
require
(
inputR1
!=
null
,
"Missing
output directory
on mapping module"
)
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
)
Logging
.
addError
(
s
"Input R1 is a empty file: $inputR1"
)
inputR2
.
foreach
(
r
=>
if
(
r
.
exists
()
&&
r
.
length
()
==
0
)
Logging
.
addError
(
s
"Input R2 is a empty file: $r"
))
inputFiles
:+=
new
InputFile
(
inputR1
)
inputR2
.
foreach
(
inputFiles
:+=
new
InputFile
(
_
))
...
...
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