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biopet.biopet
Commits
287c3a7e
Commit
287c3a7e
authored
Nov 26, 2016
by
Peter van 't Hof
Browse files
Adding main job to deps.json
parent
d0bfad15
Changes
2
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biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
View file @
287c3a7e
...
...
@@ -36,6 +36,8 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
var
executable
:
String
=
_
def
mainFunction
=
false
/** This is the default shell for drmaa jobs */
def
defaultRemoteCommand
=
"bash"
private
val
remoteCommand
:
String
=
config
(
"remote_command"
,
default
=
defaultRemoteCommand
)
...
...
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/WriteDependencies.scala
View file @
287c3a7e
...
...
@@ -110,6 +110,9 @@ object WriteDependencies extends Logging with Configurable {
name
->
Map
(
"command"
->
(
f
match
{
case
cmd
:
CommandLineFunction
=>
cmd
.
commandLine
case
_
=>
None
}),
"main_job"
->
(
f
match
{
case
cmd
:
BiopetCommandLineFunction
=>
cmd
.
mainFunction
case
_
=>
false
}),
"intermediate"
->
f
.
isIntermediate
,
"depends_on_intermediate"
->
f
.
inputs
.
exists
(
files
(
_
).
isIntermediate
),
"depends_on_jobs"
->
f
.
inputs
.
toList
.
flatMap
(
files
(
_
).
outputJobNames
).
distinct
,
...
...
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