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biopet.biopet
Commits
d4e45996
Commit
d4e45996
authored
Aug 14, 2015
by
Peter van 't Hof
Browse files
Added a option to not keep the last fastq file anymore
parent
0ae99234
Changes
1
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Inline
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public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
View file @
d4e45996
...
...
@@ -37,6 +37,9 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
/** Skip Clip fastq files */
var
skipClip
:
Boolean
=
config
(
"skip_clip"
,
default
=
false
)
/** Make a final fastq files, by default only when flexiprep is the main pipeline */
var
keepQcFastqFiles
:
Boolean
=
config
(
"keepQcFastqFiles"
,
default
=
root
==
null
)
/** Location of summary file */
def
summaryFile
=
new
File
(
outputDir
,
sampleId
.
getOrElse
(
"x"
)
+
"-"
+
libId
.
getOrElse
(
"x"
)
+
".qc.summary.json"
)
...
...
@@ -264,13 +267,13 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
val
R1
=
new
File
(
outputDir
,
R1_name
+
".qc"
+
R1_ext
+
".gz"
)
val
R2
=
new
File
(
outputDir
,
R2_name
+
".qc"
+
R2_ext
+
".gz"
)
add
(
Gzip
(
this
,
fastq_R1
,
R1
))
if
(
paired
)
add
(
Gzip
(
this
,
fastq_R2
,
R2
))
if
(!
skipTrim
||
!
skipClip
)
{
add
(
Gzip
(
this
,
fastq_R1
,
R1
),
!
keepQcFastqFiles
)
if
(
paired
)
add
(
Gzip
(
this
,
fastq_R2
,
R2
),
!
keepQcFastqFiles
)
outputFiles
+=
(
"output_R1_gzip"
->
R1
)
if
(
paired
)
outputFiles
+=
(
"output_R2_gzip"
->
R2
)
outputFiles
+=
(
"output_R1_gzip"
->
R1
)
if
(
paired
)
outputFiles
+=
(
"output_R2_gzip"
->
R2
)
if
(!
skipTrim
||
!
skipClip
)
{
fastqc_R1_after
=
Fastqc
(
this
,
R1
,
new
File
(
outputDir
,
R1_name
+
".qc.fastqc/"
))
add
(
fastqc_R1_after
)
addSummarizable
(
fastqc_R1_after
,
"fastqc_R1_qc"
)
...
...
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