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biopet.biopet
Commits
62c1705d
Commit
62c1705d
authored
Oct 09, 2015
by
Peter van 't Hof
Browse files
Fixes #213
parent
aca99bf8
Changes
1
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Inline
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public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
View file @
62c1705d
...
...
@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.core
import
java.io.File
import
nl.lumc.sasc.biopet.core.summary.
{
Summarizable
,
SummaryQScript
}
import
nl.lumc.sasc.biopet.utils.ConfigUtils
import
nl.lumc.sasc.biopet.utils.
{
Logging
,
ConfigUtils
}
import
org.broadinstitute.gatk.utils.commandline.Argument
/** This trait creates a structured way of use multisample pipelines */
...
...
@@ -90,6 +90,8 @@ trait MultiSampleQScript extends SummaryQScript {
/** Adds sample jobs */
final
def
addAndTrackJobs
()
:
Unit
=
{
if
(
sampleRegex
.
findFirstIn
(
sampleId
)
==
None
)
Logging
.
addError
(
s
"Sample '$sampleId' contains illegal chars"
)
currentSample
=
Some
(
sampleId
)
addJobs
()
qscript
.
addSummarizable
(
this
,
"pipeline"
,
Some
(
sampleId
))
...
...
@@ -129,6 +131,8 @@ trait MultiSampleQScript extends SummaryQScript {
/** Returns a list of all sampleIDs */
protected
def
sampleIds
:
Set
[
String
]
=
ConfigUtils
.
any2map
(
globalConfig
.
map
(
"samples"
)).
keySet
protected
lazy
val
sampleRegex
=
"""^[a-zA-Z0-9-_]+$"""
.
r
/** Runs addAndTrackJobs method for each sample */
final
def
addSamplesJobs
()
{
if
(
onlySamples
.
isEmpty
||
samples
.
forall
(
x
=>
onlySamples
.
contains
(
x
.
_1
)))
{
...
...
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