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biopet.biopet
Commits
6459b271
Commit
6459b271
authored
Mar 19, 2015
by
Peter van 't Hof
Browse files
Also change dependency for cutadept
parent
95db7a53
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 @
6459b271
...
...
@@ -166,14 +166,16 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
var
R1
:
File
=
new
File
(
R1_in
)
var
R2
:
File
=
if
(
paired
)
new
File
(
R2_in
)
else
null
var
deps
:
List
[
File
]
=
if
(
paired
)
List
(
R1
,
R2
)
else
List
(
R1
)
var
deps_R1
:
List
[
File
]
=
R1
::
Nil
var
deps_R2
:
List
[
File
]
=
if
(
paired
)
R2
::
Nil
else
Nil
def
deps
:
List
[
File
]
=
deps_R1
:::
deps_R2
val
seqtkSeq_R1
=
SeqtkSeq
(
this
,
R1
,
swapExt
(
outDir
,
R1
,
R1_ext
,
".sanger"
+
R1_ext
),
fastqc_R1
)
seqtkSeq_R1
.
isIntermediate
=
true
add
(
seqtkSeq_R1
)
addSummarizable
(
seqtkSeq_R1
,
"seqtkSeq_R1"
)
R1
=
seqtkSeq_R1
.
output
deps
::=
R1
deps
_R1
::=
R1
if
(
paired
)
{
val
seqtkSeq_R2
=
SeqtkSeq
(
this
,
R2
,
swapExt
(
outDir
,
R2
,
R2_ext
,
".sanger"
+
R2_ext
),
fastqc_R2
)
...
...
@@ -181,19 +183,19 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
add
(
seqtkSeq_R2
)
addSummarizable
(
seqtkSeq_R2
,
"seqtkSeq_R2"
)
R2
=
seqtkSeq_R2
.
output
deps
::=
R2
deps
_R2
::=
R2
}
val
seqstat_R1
=
Seqstat
(
this
,
R1
,
outDir
)
seqstat_R1
.
isIntermediate
=
true
seqstat_R1
.
deps
=
deps
seqstat_R1
.
deps
=
deps
_R1
add
(
seqstat_R1
)
addSummarizable
(
seqstat_R1
,
"seqstat_R1"
)
if
(
paired
)
{
val
seqstat_R2
=
Seqstat
(
this
,
R2
,
outDir
)
seqstat_R2
.
isIntermediate
=
true
seqstat_R2
.
deps
=
deps
seqstat_R2
.
deps
=
deps
_R2
add
(
seqstat_R2
)
addSummarizable
(
seqstat_R2
,
"seqstat_R2"
)
}
...
...
@@ -203,10 +205,11 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
val
cutadapt_R1
=
Cutadapt
(
this
,
R1
,
swapExt
(
outDir
,
R1
,
R1_ext
,
".clip"
+
R1_ext
))
cutadapt_R1
.
fastqc
=
fastqc_R1
cutadapt_R1
.
isIntermediate
=
true
cutadapt_R1
.
deps
=
deps_R1
add
(
cutadapt_R1
)
addSummarizable
(
cutadapt_R1
,
"clipping_R1"
)
R1
=
cutadapt_R1
.
fastq_output
deps
::=
R1
deps
_R1
::=
R1
outputFiles
+=
(
"cutadapt_R1_stats"
->
cutadapt_R1
.
stats_output
)
if
(
paired
)
{
...
...
@@ -214,10 +217,11 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
outputFiles
+=
(
"cutadapt_R2_stats"
->
cutadapt_R2
.
stats_output
)
cutadapt_R2
.
fastqc
=
fastqc_R2
cutadapt_R2
.
isIntermediate
=
true
cutadapt_R2
.
deps
=
deps_R2
add
(
cutadapt_R2
)
addSummarizable
(
cutadapt_R2
,
"clipping_R2"
)
R2
=
cutadapt_R2
.
fastq_output
deps
::=
R2
deps
_R2
::=
R2
val
fqSync
=
new
FastqSync
(
this
)
fqSync
.
refFastq
=
cutadapt_R1
.
fastq_input
...
...
@@ -232,7 +236,8 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
outputFiles
+=
(
"syncStats"
->
fqSync
.
outputStats
)
R1
=
fqSync
.
outputFastq1
R2
=
fqSync
.
outputFastq2
deps
:::=
R1
::
R2
::
Nil
deps_R1
::=
R1
deps_R2
::=
R2
}
}
...
...
@@ -255,13 +260,13 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
}
val
seqstat_R1_after
=
Seqstat
(
this
,
R1
,
outDir
)
seqstat_R1_after
.
deps
=
deps
seqstat_R1_after
.
deps
=
deps
_R1
add
(
seqstat_R1_after
)
addSummarizable
(
seqstat_R1_after
,
"seqstat_R1_after"
)
if
(
paired
)
{
val
seqstat_R2_after
=
Seqstat
(
this
,
R2
,
outDir
)
seqstat_R2_after
.
deps
=
deps
seqstat_R2_after
.
deps
=
deps
_R2
add
(
seqstat_R2_after
)
addSummarizable
(
seqstat_R2_after
,
"seqstat_R2_after"
)
}
...
...
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