Skip to content
GitLab
Projects
Groups
Snippets
/
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
Mirrors
biopet.biopet
Commits
4a9e765c
Commit
4a9e765c
authored
Feb 03, 2015
by
bow
Browse files
Use Option[File] for optional files and fix bug with adapter sequence from fastqc capture
parent
1aca9cd6
Changes
2
Hide whitespace changes
Inline
Side-by-side
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
View file @
4a9e765c
...
...
@@ -25,10 +25,10 @@ import nl.lumc.sasc.biopet.core.config.Configurable
class
Fastqc
(
val
root
:
Configurable
)
extends
BiopetCommandLineFunction
{
@Input
(
doc
=
"Contaminants"
,
required
=
false
)
var
contaminants
:
File
=
_
var
contaminants
:
Option
[
File
]
=
None
@Input
(
doc
=
"Adapters"
,
required
=
false
)
var
adapters
:
File
=
_
var
adapters
:
Option
[
File
]
=
None
@Input
(
doc
=
"Fastq file"
,
shortName
=
"FQ"
)
var
fastqfile
:
File
=
_
...
...
@@ -50,17 +50,19 @@ class Fastqc(val root: Configurable) extends BiopetCommandLineFunction {
override
def
afterGraph
{
this
.
checkExecutable
if
(
contaminants
==
null
)
{
val
fastqcDir
=
executable
.
substring
(
0
,
executable
.
lastIndexOf
(
"/"
))
val
defaultContams
=
getVersion
match
{
case
"v0.11.2"
=>
new
File
(
fastqcDir
+
"/Configuration/contaminant_list.txt"
)
case
_
=>
new
File
(
fastqcDir
+
"/Contaminants/contaminant_list.txt"
)
}
val
defaultAdapters
=
getVersion
match
{
case
"v0.11.2"
=>
new
File
(
fastqcDir
+
"/Configuration/adapter_list.txt"
)
case
_
=>
null
}
contaminants
=
config
(
"contaminants"
,
default
=
defaultContams
)
contaminants
=
contaminants
match
{
case
None
=>
val
fastqcDir
=
executable
.
substring
(
0
,
executable
.
lastIndexOf
(
"/"
))
val
defaultContams
=
getVersion
match
{
case
"v0.11.2"
=>
Option
(
new
File
(
fastqcDir
+
"/Configuration/contaminant_list.txt"
))
case
_
=>
Option
(
new
File
(
fastqcDir
+
"/Contaminants/contaminant_list.txt"
))
}
val
defaultAdapters
=
getVersion
match
{
case
"v0.11.2"
=>
Option
(
new
File
(
fastqcDir
+
"/Configuration/adapter_list.txt"
))
case
_
=>
None
}
config
(
"contaminants"
,
default
=
defaultContams
)
case
wrapped
@
Some
(
_
)
=>
wrapped
}
}
...
...
@@ -74,6 +76,6 @@ class Fastqc(val root: Configurable) extends BiopetCommandLineFunction {
conditional
(
noextract
,
"--noextract"
)
+
conditional
(
extract
,
"--extract"
)
+
conditional
(
quiet
,
"--quiet"
)
+
required
(
"-o"
,
output
.
getParent
()
)
+
required
(
"-o"
,
output
.
getParent
)
+
required
(
fastqfile
)
}
public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala
View file @
4a9e765c
...
...
@@ -99,13 +99,16 @@ class Fastqc(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Fastqc(r
def
foundAdapters
:
Set
[
AdapterSequence
]
=
{
/** Returns a list of adapter and/or contaminant sequences known to FastQC */
def
getFastqcSeqs
(
file
:
File
)
:
Set
[
AdapterSequence
]
=
if
(
file
!=
null
)
{
(
for
(
line
<-
Source
.
fromFile
(
file
).
getLines
();
if
line
.
startsWith
(
"#"
);
values
=
line
.
split
(
"\t*"
)
if
values
.
size
>=
2
)
yield
AdapterSequence
(
values
(
0
),
values
(
1
))).
toSet
}
else
Set
.
empty
[
AdapterSequence
]
def
getFastqcSeqs
(
file
:
Option
[
File
])
:
Set
[
AdapterSequence
]
=
file
match
{
case
None
=>
Set
.
empty
[
AdapterSequence
]
case
Some
(
f
)
=>
(
for
{
line
<-
Source
.
fromFile
(
f
).
getLines
()
if
!
line
.
startsWith
(
"#"
)
values
=
line
.
split
(
"\t*"
)
if
values
.
size
>=
2
}
yield
AdapterSequence
(
values
(
0
),
values
(
1
))).
toSet
}
val
found
=
qcModules
.
get
(
"Overrepresented sequences"
)
match
{
case
None
=>
Array
.
empty
[
String
]
...
...
@@ -137,7 +140,8 @@ class Fastqc(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Fastqc(r
"plot_per_sequence_quality"
->
"Images/per_sequence_quality.png"
,
"plot_sequence_length_distribution"
->
"Images/sequence_length_distribution.png"
,
"fastqc_data"
->
"fastqc_data.txt"
)
.
map
{
case
(
name
,
relPath
)
=>
.
map
{
case
(
name
,
relPath
)
=>
name
->
Map
(
"path"
->
(
outputDir
+
relPath
))
}
...
...
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment