From 133cd4852262551118a21ebc38db58b65958e6f2 Mon Sep 17 00:00:00 2001
From: bow <bow@bow.web.id>
Date: Mon, 9 Mar 2015 11:22:19 +0100
Subject: [PATCH] Force version retrieval and path resolution in CustomVarscan
---
.../biopet/pipelines/gentrap/extensions/CustomVarScan.scala | 5 ++++-
1 file changed, 4 insertions(+), 1 deletion(-)
diff --git a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/extensions/CustomVarScan.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/extensions/CustomVarScan.scala
index b3252d243..d403dea1b 100644
--- a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/extensions/CustomVarScan.scala
+++ b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/extensions/CustomVarScan.scala
@@ -66,7 +66,10 @@ class CustomVarScan(val root: Configurable) extends BiopetCommandLineFunction {
require(output.toString.endsWith(".gz"), "Output must have a .gz file extension")
}
- def cmdLine: String =
+ def cmdLine: String = {
+ // FIXME: manual trigger of commandLine for version retrieval
+ mpileup.commandLine
mpileup.cmdPipe + " | " + fixMpileup.commandLine + " | " + removeEmptyPile.commandLine + " | " +
varscan.commandLine + " | " + compress.commandLine + " && " + index.commandLine
+ }
}
--
GitLab