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biopet.biopet
Commits
c5f4ca8b
Commit
c5f4ca8b
authored
Aug 12, 2014
by
Peter van 't Hof
Browse files
Fix compile errors
parent
038301cc
Changes
1
Hide whitespace changes
Inline
Side-by-side
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cufflinks.scala
View file @
c5f4ca8b
...
...
@@ -16,7 +16,7 @@ import nl.lumc.sasc.biopet.core.config.Configurable
* Written based on cufflinks version v2.2.1.
*/
class
Cufflinks
(
val
root
:
Configurable
)
extends
BiopetCommandLineFunction
{
/** default executable */
executable
=
config
(
"exe"
,
default
=
"cufflinks"
)
...
...
@@ -31,7 +31,7 @@ class Cufflinks(val root: Configurable) extends BiopetCommandLineFunction {
if
(
input
==
null
||
output_dir
==
null
)
throw
new
RuntimeException
(
"Unexpected error when trying to set cufflinks GTF output"
)
// cufflinks always outputs a transcripts.gtf file in the output directory
output_dir
.
getCanonicalPath
()
+
File
.
pathSeparator
+
"transcripts.gtf"
new
File
(
output_dir
+
File
.
pathSeparator
+
"transcripts.gtf"
)
}
@Output
(
doc
=
"Output isoform FPKM file"
)
...
...
@@ -39,7 +39,7 @@ class Cufflinks(val root: Configurable) extends BiopetCommandLineFunction {
if
(
input
==
null
||
output_dir
==
null
)
throw
new
RuntimeException
(
"Unexpected error when trying to set cufflinks isoform FPKM output"
)
// cufflinks always outputs a isoforms.fpkm_tracking file in the output directory
output_dir
.
getCanonicalPath
()
+
File
.
pathSeparator
+
"isoforms.fpkm_tracking"
new
File
(
output_dir
+
File
.
pathSeparator
+
"isoforms.fpkm_tracking"
)
}
@Output
(
doc
=
"Output GTF file"
)
...
...
@@ -47,11 +47,11 @@ class Cufflinks(val root: Configurable) extends BiopetCommandLineFunction {
if
(
input
==
null
||
output_dir
==
null
)
throw
new
RuntimeException
(
"Unexpected error when trying to set cufflinks genes FPKM output"
)
// cufflinks always outputs a genes.fpkm_tracking file in the output directory
output_dir
.
getCanonicalPath
()
+
File
.
pathSeparator
+
"genes.fpkm_tracking"
new
File
(
output_dir
+
File
.
pathSeparator
+
"genes.fpkm_tracking"
)
}
/** write all output files to this directory [./] */
var
output_dir
:
String
=
config
(
"output_dir"
,
required
=
true
)
var
output_dir
:
String
=
_
/** number of threads used during analysis [1] */
var
num_threads
:
Option
[
Int
]
=
config
(
"num_threads"
)
...
...
@@ -72,7 +72,7 @@ class Cufflinks(val root: Configurable) extends BiopetCommandLineFunction {
var
frag_bias_correct
:
String
=
config
(
"frag_bias_correct"
)
/** use 'rescue method' for multi-reads (more accurate) [FALSE] */
var
multi_read_correct
:
Bool
=
config
(
"multi_read_correct"
)
var
multi_read_correct
:
Bool
ean
=
config
(
"multi_read_correct"
)
/** library prep used for input reads [below] */
var
library_type
:
String
=
config
(
"library_type"
)
...
...
@@ -90,10 +90,10 @@ class Cufflinks(val root: Configurable) extends BiopetCommandLineFunction {
var
max_mle_iterations
:
Option
[
Int
]
=
config
(
"max_mle_iterations"
)
/** count hits compatible with reference RNAs only [FALSE] */
var
compatible_hits_norm
:
Bool
=
config
(
"compatible_hits_norm"
)
var
compatible_hits_norm
:
Bool
ean
=
config
(
"compatible_hits_norm"
)
/** count all hits for normalization [TRUE] */
var
total_hits_norm
:
Bool
=
config
(
"total_hits_norm"
)
var
total_hits_norm
:
Bool
ean
=
config
(
"total_hits_norm"
)
/** Number of fragment generation samples [100] */
var
num_frag_count_draws
:
Option
[
Int
]
=
config
(
"num_frag_count_draws"
)
...
...
@@ -105,10 +105,10 @@ class Cufflinks(val root: Configurable) extends BiopetCommandLineFunction {
var
max_frag_multihits
:
String
=
config
(
"max_frag_multihits"
)
/** No effective length correction [FALSE] */
var
no_effective_length_correction
:
Bool
=
config
(
"no_effective_length_correction"
)
var
no_effective_length_correction
:
Bool
ean
=
config
(
"no_effective_length_correction"
)
/** No length correction [FALSE] */
var
no_length_correction
:
Bool
=
config
(
"no_length_correction"
)
var
no_length_correction
:
Bool
ean
=
config
(
"no_length_correction"
)
/** assembled transcripts have this ID prefix [CUFF] */
var
label
:
String
=
config
(
"label"
)
...
...
@@ -156,7 +156,7 @@ class Cufflinks(val root: Configurable) extends BiopetCommandLineFunction {
var
overlap_radius
:
Option
[
Int
]
=
config
(
"overlap_radius"
)
/** disable tiling by faux reads [FALSE] */
var
no_faux_reads
:
Bool
=
config
(
"no_faux_reads"
)
var
no_faux_reads
:
Bool
ean
=
config
(
"no_faux_reads"
)
/** overhang allowed on 3' end when merging with reference [600] */
var
flag_3_overhang_tolerance
:
Option
[
Int
]
=
config
(
"flag_3_overhang_tolerance"
)
...
...
@@ -165,13 +165,13 @@ class Cufflinks(val root: Configurable) extends BiopetCommandLineFunction {
var
intron_overhang_tolerance
:
Option
[
Int
]
=
config
(
"intron_overhang_tolerance"
)
/** log-friendly verbose processing (no progress bar) [FALSE] */
var
verbose
:
Bool
=
config
(
"verbose"
)
var
verbose
:
Bool
ean
=
config
(
"verbose"
)
/** log-friendly quiet processing (no progress bar) [FALSE] */
var
quiet
:
Bool
=
config
(
"quiet"
)
var
quiet
:
Bool
ean
=
config
(
"quiet"
)
/** do not contact server to check for update availability [FALSE] */
var
no_update_check
:
Bool
=
config
(
"no_update_check"
)
var
no_update_check
:
Bool
ean
=
config
(
"no_update_check"
)
override
val
versionRegex
=
"""cufflinks v(.*)"""
.
r
override
def
versionCommand
=
executable
...
...
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