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biopet.biopet
Commits
449202bd
Commit
449202bd
authored
Jan 27, 2015
by
Peter van 't Hof
Browse files
Remove queue args from pipeline
parent
8f104889
Changes
1
Hide whitespace changes
Inline
Side-by-side
public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
View file @
449202bd
...
...
@@ -32,16 +32,16 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
@Input
(
doc
=
"R2 fastq file (gzipped allowed)"
,
shortName
=
"R2"
,
required
=
false
)
var
input_R2
:
File
=
_
@Argument
(
doc
=
"
Skip Trim fastq files
"
,
shortName
=
"skiptrim"
,
required
=
false
)
var
skipTrim
:
Boolean
=
config
(
"skiptrim"
,
default
=
false
)
/**
Skip Trim fastq files
*/
var
skipTrim
:
Boolean
=
config
(
"skip
_
trim"
,
default
=
false
)
@Argument
(
doc
=
"
Skip Clip fastq files
"
,
shortName
=
"skipclip"
,
required
=
false
)
var
skipClip
:
Boolean
=
config
(
"skipclip"
,
default
=
false
)
/**
Skip Clip fastq files
*/
var
skipClip
:
Boolean
=
config
(
"skip
_
clip"
,
default
=
false
)
@Argument
(
doc
=
"Sample name"
,
shortName
=
"sample"
,
required
=
true
)
/** Sample name */
var
sampleName
:
String
=
_
@Argument
(
doc
=
"Library name"
,
shortName
=
"library"
,
required
=
true
)
/** Library name */
var
libraryName
:
String
=
_
var
paired
:
Boolean
=
(
input_R2
!=
null
)
...
...
@@ -136,24 +136,28 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
var
deps
:
List
[
File
]
=
if
(
paired
)
List
(
R1
,
R2
)
else
List
(
R1
)
val
seqtkSeq_R1
=
SeqtkSeq
(
this
,
R1
,
swapExt
(
outDir
,
R1
,
R1_ext
,
".sanger"
+
R1_ext
),
fastqc_R1
)
add
(
seqtkSeq_R1
,
isIntermediate
=
true
)
seqtkSeq_R1
.
isIntermediate
=
true
add
(
seqtkSeq_R1
)
R1
=
seqtkSeq_R1
.
output
deps
::=
R1
if
(
paired
)
{
val
seqtkSeq_R2
=
SeqtkSeq
(
this
,
R2
,
swapExt
(
outDir
,
R2
,
R2_ext
,
".sanger"
+
R2_ext
),
fastqc_R2
)
add
(
seqtkSeq_R2
,
isIntermediate
=
true
)
seqtkSeq_R2
.
isIntermediate
=
true
add
(
seqtkSeq_R2
)
R2
=
seqtkSeq_R2
.
output
deps
::=
R2
}
val
seqstat_R1
=
Seqstat
(
this
,
R1
,
outDir
)
add
(
seqstat_R1
,
isIntermediate
=
true
)
seqstat_R1
.
isIntermediate
=
true
add
(
seqstat_R1
)
summary
.
addSeqstat
(
seqstat_R1
,
R2
=
false
,
after
=
false
,
chunk
)
if
(
paired
)
{
val
seqstat_R2
=
Seqstat
(
this
,
R2
,
outDir
)
add
(
seqstat_R2
,
isIntermediate
=
true
)
seqstat_R2
.
isIntermediate
=
true
add
(
seqstat_R2
)
summary
.
addSeqstat
(
seqstat_R2
,
R2
=
true
,
after
=
false
,
chunk
)
}
...
...
@@ -161,7 +165,8 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
val
cutadapt_R1
=
Cutadapt
(
this
,
R1
,
swapExt
(
outDir
,
R1
,
R1_ext
,
".clip"
+
R1_ext
))
cutadapt_R1
.
fastqc
=
fastqc_R1
add
(
cutadapt_R1
,
isIntermediate
=
true
)
cutadapt_R1
.
isIntermediate
=
true
add
(
cutadapt_R1
)
summary
.
addCutadapt
(
cutadapt_R1
,
R2
=
false
,
chunk
)
R1
=
cutadapt_R1
.
fastq_output
deps
::=
R1
...
...
@@ -171,7 +176,8 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
val
cutadapt_R2
=
Cutadapt
(
this
,
R2
,
swapExt
(
outDir
,
R2
,
R2_ext
,
".clip"
+
R2_ext
))
outputFiles
+=
(
"cutadapt_R2_stats"
->
cutadapt_R2
.
stats_output
)
cutadapt_R2
.
fastqc
=
fastqc_R2
add
(
cutadapt_R2
,
isIntermediate
=
true
)
cutadapt_R2
.
isIntermediate
=
true
add
(
cutadapt_R2
)
summary
.
addCutadapt
(
cutadapt_R2
,
R2
=
true
,
chunk
)
R2
=
cutadapt_R2
.
fastq_output
deps
::=
R2
...
...
@@ -179,7 +185,8 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
val
fastqSync
=
FastqSync
(
this
,
cutadapt_R1
.
fastq_input
,
cutadapt_R1
.
fastq_output
,
cutadapt_R2
.
fastq_output
,
swapExt
(
outDir
,
R1
,
R1_ext
,
".sync"
+
R1_ext
),
swapExt
(
outDir
,
R2
,
R2_ext
,
".sync"
+
R2_ext
),
swapExt
(
outDir
,
R1
,
R1_ext
,
".sync.stats"
))
fastqSync
.
deps
:::=
deps
add
(
fastqSync
,
isIntermediate
=
true
)
fastqSync
.
isIntermediate
=
true
add
(
fastqSync
)
summary
.
addFastqcSync
(
fastqSync
,
chunk
)
outputFiles
+=
(
"syncStats"
->
fastqSync
.
output_stats
)
R1
=
fastqSync
.
output_R1
...
...
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