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biopet.biopet
Commits
53240be8
Commit
53240be8
authored
Jan 30, 2017
by
Peter van 't Hof
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Changed name in extension
parent
2364d858
Changes
2
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2 changed files
with
5 additions
and
4 deletions
+5
-4
biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/DownloadNcbiAssembly.scala
...c/sasc/biopet/extensions/tools/DownloadNcbiAssembly.scala
+3
-2
generate-indexes/src/main/scala/nl/lumc/sasc/biopet/pipelines/generateindexes/DownloadGenomes.scala
...sc/biopet/pipelines/generateindexes/DownloadGenomes.scala
+2
-2
No files found.
biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/DownloadNcbiAssembly.scala
View file @
53240be8
...
...
@@ -31,7 +31,8 @@ class DownloadNcbiAssembly(val root: Configurable) extends ToolCommandFunction {
var
outputReport
:
File
=
_
var
assemblyId
:
String
=
null
@Input
(
required
=
true
)
var
assemblyReport
:
File
=
null
var
nameHeader
:
Option
[
String
]
=
None
...
...
@@ -41,7 +42,7 @@ class DownloadNcbiAssembly(val root: Configurable) extends ToolCommandFunction {
override
def
defaultCoreMemory
=
4.0
override
def
cmdLine
=
super
.
cmdLine
+
required
(
"-a"
,
assembly
Id
)
+
required
(
"-a"
,
assembly
Report
)
+
required
(
"--report"
,
outputReport
)
+
required
(
"-o"
,
output
)
+
optional
(
"--nameHeader"
,
nameHeader
)
+
...
...
generate-indexes/src/main/scala/nl/lumc/sasc/biopet/pipelines/generateindexes/DownloadGenomes.scala
View file @
53240be8
...
...
@@ -65,9 +65,9 @@ class DownloadGenomes(val root: Configurable) extends QScript with BiopetQScript
val
downloadFastaFile
=
new
File
(
genomeDir
,
"download.reference.fa"
)
genomeConfig
.
get
(
"ncbi_assembly_report"
)
match
{
case
Some
(
assembly
ID
:
String
)
=>
case
Some
(
assembly
Report
:
String
)
=>
val
downloadAssembly
=
new
DownloadNcbiAssembly
(
this
)
downloadAssembly
.
assembly
Id
=
assemblyID
downloadAssembly
.
assembly
Report
=
new
File
(
assemblyReport
)
downloadAssembly
.
output
=
downloadFastaFile
downloadAssembly
.
outputReport
=
new
File
(
genomeDir
,
s
"$speciesName-$genomeName.assembly.report"
)
downloadAssembly
.
nameHeader
=
genomeConfig
.
get
(
"ncbi_assembly_header_name"
).
map
(
_
.
toString
)
...
...
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