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biopet.biopet
Commits
18bc6d01
Commit
18bc6d01
authored
Jun 13, 2016
by
Peter van 't Hof
Browse files
Fixed sample and library check
parent
63029298
Changes
1
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Inline
Side-by-side
flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
View file @
18bc6d01
...
...
@@ -16,11 +16,11 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep
import
nl.lumc.sasc.biopet.core.summary.SummaryQScript
import
nl.lumc.sasc.biopet.core.
{
BiopetFifoPipe
,
PipelineCommand
,
SampleLibraryTag
}
import
nl.lumc.sasc.biopet.extensions.
{
Zcat
,
Gzip
}
import
nl.lumc.sasc.biopet.extensions.
{
Gzip
,
Zcat
}
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
nl.lumc.sasc.biopet.utils.IoUtils._
import
nl.lumc.sasc.biopet.extensions.tools.
{
Validate
Fastq
,
SeqStat
,
Fastq
Sync
}
import
nl.lumc.sasc.biopet.extensions.tools.
{
Fastq
Sync
,
SeqStat
,
Validate
Fastq
}
import
nl.lumc.sasc.biopet.utils.Logging
import
org.broadinstitute.gatk.queue.QScript
class
Flexiprep
(
val
root
:
Configurable
)
extends
QScript
with
SummaryQScript
with
SampleLibraryTag
{
...
...
@@ -74,10 +74,9 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
/** Function that's need to be executed before the script is accessed */
def
init
()
{
require
(
outputDir
!=
null
,
"Missing output directory on flexiprep module"
)
require
(
inputR1
!=
null
,
"Missing input R1 on flexiprep module"
)
require
(
sampleId
!=
null
,
"Missing sample ID on flexiprep module"
)
require
(
libId
!=
null
,
"Missing library ID on flexiprep module"
)
if
(
inputR1
==
null
)
Logging
.
addError
(
"Missing input R1 on flexiprep module"
)
if
(
sampleId
==
null
||
sampleId
==
None
)
Logging
.
addError
(
"Missing sample ID on flexiprep module"
)
if
(
libId
==
null
||
libId
==
None
)
Logging
.
addError
(
"Missing library ID on flexiprep module"
)
paired
=
inputR2
.
isDefined
...
...
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