Skip to content
GitLab
Projects
Groups
Snippets
Help
Loading...
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
B
biopet.biopet
Project overview
Project overview
Details
Activity
Releases
Repository
Repository
Files
Commits
Branches
Tags
Contributors
Graph
Compare
CI / CD
CI / CD
Pipelines
Jobs
Schedules
Operations
Operations
Environments
Analytics
Analytics
CI / CD
Repository
Value Stream
Members
Members
Collapse sidebar
Close sidebar
Activity
Graph
Jobs
Commits
Open sidebar
Mirrors
biopet.biopet
Commits
3c83710e
Commit
3c83710e
authored
Mar 29, 2017
by
Peter van 't Hof
Committed by
GitHub
Mar 29, 2017
Browse files
Options
Browse Files
Download
Plain Diff
Merge pull request #49 from biopet/fix-pipes
Fix pipes
parents
23dbd3ee
8d5a16f5
Changes
2
Hide whitespace changes
Inline
Side-by-side
Showing
2 changed files
with
12 additions
and
8 deletions
+12
-8
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsFlagstat.scala
...mc/sasc/biopet/extensions/samtools/SamtoolsFlagstat.scala
+3
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsView.scala
...l/lumc/sasc/biopet/extensions/samtools/SamtoolsView.scala
+9
-7
No files found.
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsFlagstat.scala
View file @
3c83710e
...
...
@@ -28,7 +28,9 @@ class SamtoolsFlagstat(val root: Configurable) extends Samtools {
var
output
:
File
=
_
/** Returns command to execute */
def
cmdLine
=
required
(
executable
)
+
required
(
"flagstat"
)
+
required
(
input
)
+
" > "
+
required
(
output
)
def
cmdLine
=
required
(
executable
)
+
required
(
"flagstat"
)
+
(
if
(
inputAsStdin
)
"-"
else
required
(
input
))
+
(
if
(
outputAsStsout
)
""
else
" > "
+
required
(
output
))
}
object
SamtoolsFlagstat
{
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsView.scala
View file @
3c83710e
...
...
@@ -33,18 +33,20 @@ class SamtoolsView(val root: Configurable) extends Samtools {
var
f
:
List
[
String
]
=
config
(
"f"
,
default
=
List
.
empty
[
String
])
var
F
:
List
[
String
]
=
config
(
"F"
,
default
=
List
.
empty
[
String
])
def
cmdBase
=
required
(
executable
)
+
@Input
(
required
=
false
)
var
L
:
Option
[
File
]
=
None
/** Returns command to execute */
def
cmdLine
=
required
(
executable
)
+
required
(
"view"
)
+
optional
(
"-q"
,
q
)
+
optional
(
"-L"
,
L
)
+
repeat
(
"-f"
,
f
)
+
repeat
(
"-F"
,
F
)
+
conditional
(
b
,
"-b"
)
+
conditional
(
h
,
"-h"
)
def
cmdPipeInput
=
cmdBase
+
"-"
def
cmdPipe
=
cmdBase
+
required
(
input
)
/** Returns command to execute */
def
cmdLine
=
cmdPipe
+
" > "
+
required
(
output
)
conditional
(
h
,
"-h"
)
+
(
if
(
inputAsStdin
)
"-"
else
required
(
input
))
+
(
if
(
outputAsStsout
)
""
else
" > "
+
required
(
output
))
}
object
SamtoolsView
{
...
...
Write
Preview
Markdown
is supported
0%
Try again
or
attach a new file
.
Attach a 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