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biopet.biopet
Commits
e04af32c
Commit
e04af32c
authored
Feb 25, 2016
by
Peter van 't Hof
Browse files
Added option to skip abort step
parent
b4025176
Changes
1
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Inline
Side-by-side
public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
View file @
e04af32c
...
...
@@ -120,10 +120,12 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
validateFastq
.
jobOutputFile
=
new
File
(
outputDir
,
".validate_fastq.log.out"
)
add
(
validateFastq
)
val
checkValidateFastq
=
new
CheckValidateFastq
checkValidateFastq
.
inputLogFile
=
validateFastq
.
jobOutputFile
checkValidateFastq
.
jobOutputFile
=
new
File
(
outputDir
,
".check.validate_fastq.log.out"
)
add
(
checkValidateFastq
)
if
(
config
(
"abort_on_corrupt_fastq"
,
default
=
true
))
{
val
checkValidateFastq
=
new
CheckValidateFastq
checkValidateFastq
.
inputLogFile
=
validateFastq
.
jobOutputFile
checkValidateFastq
.
jobOutputFile
=
new
File
(
outputDir
,
".check.validate_fastq.log.out"
)
add
(
checkValidateFastq
)
}
if
(
paired
)
{
fastqc_R2
=
Fastqc
(
this
,
input_R2
.
get
,
new
File
(
outputDir
,
R2_name
+
".fastqc/"
))
...
...
@@ -271,10 +273,12 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
validateFastq
.
jobOutputFile
=
new
File
(
outputDir
,
".validate_fastq.qc.log.out"
)
add
(
validateFastq
)
val
checkValidateFastq
=
new
CheckValidateFastq
checkValidateFastq
.
inputLogFile
=
validateFastq
.
jobOutputFile
checkValidateFastq
.
jobOutputFile
=
new
File
(
outputDir
,
".check.validate_fastq.qc.log.out"
)
add
(
checkValidateFastq
)
if
(
config
(
"abort_on_corrupt_fastq"
,
default
=
true
))
{
val
checkValidateFastq
=
new
CheckValidateFastq
checkValidateFastq
.
inputLogFile
=
validateFastq
.
jobOutputFile
checkValidateFastq
.
jobOutputFile
=
new
File
(
outputDir
,
".check.validate_fastq.qc.log.out"
)
add
(
checkValidateFastq
)
}
outputFiles
+=
(
"output_R1_gzip"
->
fastqR1Qc
)
if
(
paired
)
outputFiles
+=
(
"output_R2_gzip"
->
fastqR2Qc
.
get
)
...
...
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