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biopet.biopet
Commits
5a635225
Commit
5a635225
authored
Feb 17, 2015
by
Peter van 't Hof
Browse files
Added plots to outputFiles
parent
273e70f5
Changes
1
Hide whitespace changes
Inline
Side-by-side
public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala
View file @
5a635225
...
...
@@ -19,6 +19,7 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep
import
java.io.
{
File
,
FileNotFoundException
}
import
nl.lumc.sasc.biopet.core.summary.Summarizable
import
org.broadinstitute.gatk.utils.commandline.Output
import
scala.io.Source
...
...
@@ -167,8 +168,11 @@ class Fastqc(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Fastqc(r
ConfigUtils
.
mapToJson
(
outputMap
)
}
@Output
var
outputFiles
:
List
[
File
]
=
Nil
def
summaryFiles
:
Map
[
String
,
File
]
=
{
Map
(
"plot_duplication_levels"
->
(
"Images"
+
File
.
separator
+
"duplication_levels.png"
),
val
outputFiles
=
Map
(
"plot_duplication_levels"
->
(
"Images"
+
File
.
separator
+
"duplication_levels.png"
),
"plot_kmer_profiles"
->
(
"Images"
+
File
.
separator
+
"kmer_profiles.png"
),
"plot_per_base_gc_content"
->
(
"Images"
+
File
.
separator
+
"per_base_gc_content.png"
),
"plot_per_base_n_content"
->
(
"Images"
+
File
.
separator
+
"per_base_n_content.png"
),
...
...
@@ -178,7 +182,11 @@ class Fastqc(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Fastqc(r
"plot_per_sequence_quality"
->
(
"Images"
+
File
.
separator
+
"per_sequence_quality.png"
),
"plot_sequence_length_distribution"
->
(
"Images"
+
File
.
separator
+
"sequence_length_distribution.png"
),
"fastqc_data"
->
(
"fastqc_data.txt"
))
.
map
(
x
=>
(
x
.
_1
->
new
File
(
outputDir
,
x
.
_2
)))
++
Map
(
"fastq_file"
->
this
.
fastqfile
)
.
map
(
x
=>
(
x
.
_1
->
new
File
(
outputDir
,
x
.
_2
)))
outputFiles
.
foreach
(
this
.
outputFiles
:+=
_
.
_2
)
outputFiles
++
Map
(
"fastq_file"
->
this
.
fastqfile
)
}
def
summaryData
:
Map
[
String
,
Any
]
=
Map
(
"version"
->
getVersion
)
...
...
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