From ef29ace564832f78494d52a113be8b02c4bb237f Mon Sep 17 00:00:00 2001
From: Wai Yi Leung <w.y.leung@lumc.nl>
Date: Mon, 18 Jan 2016 13:27:43 +0100
Subject: [PATCH] Pindel outputpath fix.
---
.../biopet/extensions/pindel/PindelCaller.scala | 13 +++++--------
1 file changed, 5 insertions(+), 8 deletions(-)
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelCaller.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelCaller.scala
index c7c17583a..0ccb2468b 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelCaller.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelCaller.scala
@@ -31,7 +31,7 @@ import org.broadinstitute.gatk.utils.commandline._
class PindelCaller(val root: Configurable) extends BiopetCommandLineFunction with Reference with Version {
executable = config("exe", default = "pindel")
- override def defaultCoreMemory = 3.0
+ override def defaultCoreMemory = 4.0
override def defaultThreads = 4
override def versionRegex = """Pindel version:? (.*)""".r
@@ -123,18 +123,16 @@ class PindelCaller(val root: Configurable) extends BiopetCommandLineFunction wit
}
}
- // modify `output_prefix` to include samplename
- output_prefix = new File(output_prefix + File.separator, "sample")
-
- // set the output file
- output_file = new File(output_prefix, "_D")
+ // set the output file, the DELetion call is always made
+ // TODO: add more outputs for the LI, SI, INV etc...
+ output_file = new File(output_prefix + File.separator, "sample_D")
}
def cmdLine = required(executable) +
required("--fasta ", reference) +
optional("--pindel-config-file", pindel_file) +
optional("--config-file", config_file) +
- required("--output-prefix ", output_prefix) +
+ required("--output-prefix ", new File(output_prefix + File.separator, "sample")) +
optional("--RP", RP) +
optional("--min_distance_to_the_end", min_distance_to_the_end) +
optional("--number_of_threads", threads) +
@@ -167,7 +165,6 @@ class PindelCaller(val root: Configurable) extends BiopetCommandLineFunction wit
conditional(genotyping, "-g") +
optional("--output_of_breakdancer_events", output_of_breakdancer_events) +
optional("--name_of_logfile", name_of_logfile) +
- optional("--number_of_threads", threads) +
optional("--Ploidy", Ploidy) +
conditional(detect_DD, "detect_DD") +
optional("--MAX_DD_BREAKPOINT_DISTANCE", MAX_DD_BREAKPOINT_DISTANCE) +
--
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