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biopet.biopet
Commits
ca9c7e5c
Commit
ca9c7e5c
authored
Oct 09, 2015
by
Peter van 't Hof
Browse files
Fix zcat for chunking
parent
f4f1f4cb
Changes
2
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public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Zcat.scala
View file @
ca9c7e5c
...
...
@@ -36,7 +36,7 @@ class Zcat(val root: Configurable) extends BiopetCommandLineFunction {
/** Returns command to execute */
def
cmdLine
=
required
(
executable
)
+
(
if
(
inputAsStdin
)
""
else
re
quired
(
input
))
+
(
if
(
inputAsStdin
)
""
else
re
peat
(
input
))
+
(
if
(
outputAsStsout
)
""
else
" > "
+
required
(
output
))
}
...
...
public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
View file @
ca9c7e5c
...
...
@@ -253,8 +253,14 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
throw
new
IllegalStateException
(
"R1 and R2 file number is not the same"
)
if
(
fastq_R1
.
length
>
1
)
{
add
(
Zcat
(
this
,
fastq_R1
,
fastqR1Qc
)
|
new
Gzip
(
this
)
>
fastqR1Qc
)
if
(
paired
)
add
(
Zcat
(
this
,
fastq_R2
,
fastqR2Qc
.
get
)
|
new
Gzip
(
this
)
>
fastqR2Qc
.
get
)
val
zcat
=
new
Zcat
(
this
)
zcat
.
input
=
fastq_R1
add
(
zcat
|
new
Gzip
(
this
)
>
fastqR1Qc
)
if
(
paired
)
{
val
zcat
=
new
Zcat
(
this
)
zcat
.
input
=
fastq_R2
add
(
zcat
|
new
Gzip
(
this
)
>
fastqR2Qc
.
get
)
}
}
outputFiles
+=
(
"output_R1_gzip"
->
fastqR1Qc
)
...
...
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